Glyph

Wafer Layout and Alignment Marks

A mask set isn't finished when one die looks right. Before tapeout you still need to know how that die steps across a real wafer — how many you get, how many the edge throws away — and you need alignment marks that print in the same place on every level, so a five-mask process actually lands on top of itself under the aligner. This guide covers both: Arrange → Wafer layout…, which step-and-repeats a die cell across a wafer blank with dicing lanes and an edge exclusion, and the alignment-mark pair under Verify — Place alignment marks…, which drops one mark type at a list of coordinates across several layers in a single undo step, and Check mark alignment…, a read-only geometric check that reports whether every level agrees.

Time: ~25 min

You'll need: Glyph open on a blank document — File → New if you have been editing something else. Nothing is imported and nothing is pre-supplied: steps 1 to 6 build the die, its two mask layers and their field tones from that blank document, because the wafer and mark tools downstream depend on all of it.

  1. Name the three layers. A blank document starts with three layers, 1/0, 2/0 and 3/0, named Layer 1, Layer 2 and Layer 3. The right-hand panel opens on its Layers tab; double-click a layer's name to turn it into a text box, type the new name and press Enter. Name 1/0 Active, 2/0 Metal1 and 3/0 Wafer. The name is Glyph's label for your convenience — GDS stores only the layer/datatype number pair beside it, which is why the numbers stay put while the names change.

    The Layers tab of Glyph's right-hand panel showing three rows named Active, Metal1 and Wafer with their layer numbers 1/0, 2/0 and 3/0, an opacity slider, and eye and padlock buttons on each row. The Wafer row is highlighted as the current layer.

  2. Give Metal1 a dark-field tone. Click the small hatched colour swatch at the left end of the Metal1 row — the leftmost thing on the row, about the size of the text beside it. That opens the Layer colours dialog. Under MASK FIELD TONE, click Dark field; it lights up in orange as soon as it takes, and the hint underneath states what you just declared: "Dark field → drawn shapes become chromium; clear field → drawn shapes become the openings." Leave Active unset (a layer with no declared tone is treated as clear field). This is load-bearing later: steps 11 and 12 emit a different shape on Metal1 precisely because of this setting.

    Glyph's Layer colours dialog cropped to its top: a Current row with fill and edge swatches reading #0077bb, then a Mask field tone control with three buttons — em-dash Unset, Dark field and Clear field — with Dark field selected and outlined in orange, above a hint explaining that dark field means drawn shapes become chromium.

  3. Create the die cell. Click Close in the dialog. Back in the panel, switch to the Cells tab and click the + button at the right of the CELLS header, type DIE, and press Enter. A DIE row appears below TOP. Step 2 also left a small DF badge on the Metal1 row back in the Layers tab — you'll first see it in step 5's screenshot — and that badge is how you check the tone stuck without reopening the dialog.

    The Cells tab of Glyph's right-hand panel listing two rows, TOP in bold and underlined as the cell being edited, and DIE below it, each with a shape count of 0 and an enter-cell arrow at its right end.

  4. Find the enter-cell icon. Hover the DIE row and seven small icons appear along its right end. Left to right they are: an eye (hide this cell's instances), a square (show its instances as a box), a pencil (rename), stacked cubes (insert an instance, an SREF), a 3×3 grid (insert an array, an AREF), an arrow pointing into a bracket — that is enter-cell — and a waste bin (delete). The enter arrow is the second from the right, and it is the only one of the seven that stays visible when you are not hovering. Double-clicking anywhere on the row does the same thing.

    A close strip of the hovered DIE row in the Cells panel, showing its shape count and then seven icon buttons: eye, square, pencil, stacked cubes, three-by-three grid, an arrow pointing into a bracket, and a waste bin.

  5. Enter DIE and draw the 4.4 mm active area. Click that arrow. The breadcrumb at the top-left of the canvas now shows TOP (top), a chevron, and DIE, and the hint strip along the bottom of the window says Editing DIE — Esc to go back. Two things before you draw. First, switch back to the Layers tab and click the Active row: the highlighted row is the layer new shapes land on, and after the renaming in step 1 it is still whichever row you touched last — make Active current before drawing. Second, this is the first step where you move around the canvas freely — scroll the mouse wheel to zoom at the pointer, hold Space and drag (or drag with the middle mouse button) to pan, and press Ctrl+0 for View → Zoom to fit when you have lost the drawing.

    Now arm the Box tool in the toolbar (the square icon, shortcut B) and drag out a rough square — you cannot drag an exact 4400 µm, and you don't need to. With the box still selected, type the real numbers into the PROPERTIES panel, which is authoritative: W 4400, then H 4400, then X 300, then Y 300. Width and height first, always: W and H scale the shape about its centre, so setting them afterwards would move the corner you just placed. Anchor is on Corner, so X and Y are the box's lower-left corner. The status bar reads 1 shape · 1 selected.

    The Glyph canvas inside the DIE cell showing one large orange hatched square with selection handles and inline W 4400.00 µm and H 4400.00 µm badges, the Properties panel reading X 300.00 µm, Y 300.00 µm, W 4400.00 µm, H 4400.00 µm and Layer Active (1/0), and the status bar reading 1 shape and 1 selected.

  6. Draw one metal trace on Metal1. In the Layers tab click the Metal1 row so it becomes the current layer, then arm Box again — Glyph's draw tools are one-shot, so a committed box reverts the tool to Select and a second drag without re-arming would silently marquee-select instead of drawing. Drag a rough sliver inside the active-area square, then set W 1500, H 50, X 500, Y 2350, pressing Enter after each. The Properties panel's Layer row confirms Metal1 (2/0), and the status bar reads 2 shapes · 1 selected. That 1500 µm length is deliberate: the mark check in step 13 ignores any shape whose bounding box exceeds 500 µm on either axis, so a real die feature is never mistaken for an alignment mark. Your die is done — a 5 mm × 5 mm cell with a 4.4 mm active area (a solid square — "area", not an outline) and one metal trace.

    The DIE cell with the orange hatched 4.4 mm active-area square and a thin selected horizontal trace across it carrying inline W 1500.00 µm and H 50.00 µm badges, the Properties panel reading X 500.00 µm, Y 2350.00 µm, W 1500.00 µm, H 50.00 µm and Layer Metal1 (2/0), and the status bar reading 2 shapes and 1 selected.

  7. Open the wafer planner. Click TOP (top) in the breadcrumb to leave the die, then choose Arrange → Wafer layout…. The dialog opens on the 150mm preset — 150 mm diameter, a 57.5 mm primary flat facing the bottom, the SEMI-standard shape. DIE is the only cell other than TOP, so the DIE CELL picker defaults to it and Generate is already enabled. First confirm four values every later number depends on: DIE WIDTH and DIE HEIGHT 5000, PITCH X and PITCH Y 5100 (µm). Then change two fields: set OUTLINE LAYER to 3/0 — Wafer, so the wafer rim and the dicing lanes land on their own layer instead of on a die layer, and set LANE WIDTH (µm) to 100. Note DIE ORIGIN, left on Lower-left of footprint: it says where the die cell's own origin sits inside its 5000 µm footprint, so with it on lower-left the die grid starts with a footprint corner at (0, 0) — which is what makes the mark coordinates in step 11 computable. The die fields are in µm, so 5000 is 5 mm. The stats strip already reads 553 dies as 26 AREFs, 0 SREFs, 231 dropped, computed from the numbers above with no wafer drawn yet.

    Glyph's Wafer layout dialog cropped to its panel: 150mm preset, 150 mm diameter, primary flat facing bottom at 57.5 mm, 3 mm edge exclusion, outline layer 3/0 Wafer, die cell DIE, 5000 by 5000 die size, 5100 by 5100 pitch, die origin lower-left of footprint, 100 lane width, the dicing-lanes checkbox ticked, and a stats strip reading 553 dies, 26 AREFs, 0 SREFs, 231 dropped.

  8. Watch the preview react. Type 5 into EDGE EXCLUSION (MM), replacing the 3. The stats strip updates instantly, before you have generated anything: 532 dies, 25 AREFs, 144 dropped — 21 fewer dies for 2 mm more exclusion. This is the whole point of the live preview: you can feel out edge exclusion, pitch, and lane width against the die count before committing a single shape.

    The same Wafer layout dialog with edge exclusion changed to 5 mm, the outline layer field carrying the focus ring left by tabbing out of the exclusion box, and the stats strip updated to read 532 dies, 25 AREFs, 0 SREFs, 144 dropped.

  9. Generate at 3 mm exclusion. Set edge exclusion back to 3 and click Generate. Glyph writes the wafer outline, the dicing lanes, and the die field into TOP as one undo entry: 58 plain shapes (2 for the outline, 56 lane rectangles) plus 26 AREFs — not 553 SREFs. Each AREF is one row's contiguous run of in-spec dies (cols × 1), because AREF has no sparse form and a round wafer clipped against a rectangular grid isn't one rectangle; a full 150 mm wafer at this pitch still costs only ~26 instances. The toast reads 553 dies placed as 26 AREFs + 0 SREFs across 26 rows; 231 grid positions dropped at the edge. and the status bar reads 58 shapes · 26 arrays.

    The Glyph canvas zoomed to fit the whole wafer: a circular field of orange dies with a flat cut at the bottom, a cyan wafer rim with an inner exclusion ring, cyan dicing lanes between every row and column, and a toast reading 553 dies placed as 26 AREFs plus 0 SREFs across 26 rows, 231 grid positions dropped at the edge. Status bar reads 58 shapes and 26 arrays.

  10. Look at where dies get dropped. Zoom to the bottom of the wafer, where the primary flat and the edge exclusion both cut into the die grid. Whole rows of the rectangular candidate grid simply aren't drawn there — the planner never emits a die whose footprint would cross the flat or fall inside the exclusion band, so "dropped" isn't a visual gap you have to clean up, it's positions that were never placed.

    A zoomed view of the bottom of the wafer where the flat cuts across: rows of orange dies stepping in as the flat and the curved wafer edge encroach, cyan dicing lanes between them, and empty canvas beyond the cut line where no dies were placed.

  11. Set up an alignment-mark set. Choose Verify → Place alignment marks…. Leave MARK TYPE on its default, Alignment cross (+) — a classic photolithography cross, 100 µm tip to tip with 20 µm arms. The POSITIONS (µm) box wants one x, y pair per line, which is exactly what its own first line says: # x, y in µm — one mark position per line. Keep that comment line, delete the 0, 0 under it, and type three positions:

    -40850, -40850
40750, -40850
-50, 45850

    Those numbers look arbitrary and aren't. Marks belong in the dicing streets, not on a die, and with DIE ORIGIN on lower-left the die footprints run [5100·i, 5100·i + 5000] µm on both axes — so the street between two columns is 100 µm wide (pitch 5100 minus die 5000) and centred on 5100·i + 5050 µm. Each coordinate above is a street crossing, and the 100 µm cross therefore spans its street exactly, end to end. Finally, make sure both 1/0 — ACTIVE and 2/0 — METAL1 are ticked under LAYERS — the dialog pre-ticks whichever layer is current, which is Metal1 (current since step 6), so 1/0 — ACTIVE is the one you tick yourself — and leave 3/0 — WAFER alone. The summary line reads 3 position(s) × 2 layer(s) = 6 marks, one undo entry., and because Metal1 is dark field the dialog warns that the mark is emitted there as a window — the cross knocked out of a clear surround — instead of solid geometry, so the same mark prints as the same image on a clear- and a dark-field level.

    Glyph's Place alignment marks dialog cropped to its panel: mark type Alignment cross (+), a positions box holding a comment line reading x, y in micrometres one mark position per line and three coordinate pairs, layers 1/0 ACTIVE and 2/0 METAL1 both ticked with 3/0 WAFER unticked, a summary reading 3 positions times 2 layers equals 6 marks one undo entry, and an amber note that 2/0 is a dark-field level so the mark is emitted as a window.

  12. Place the set and look at one mark. Click Place. Nine shapes land in TOP in one undo entry — six on the clear-field layer (two boxes per cross, three crosses) and three on the dark-field layer (one windowed polygon per cross) — and the toast reads Placed 6 marks (9 shapes) on 2 layers. The status bar reads 67 shapes · 26 arrays. Now navigate to the first position, -40850, -40850 µm — and use the live cursor read-out at the bottom-left of the status bar (x … · y …) as your compass: zoom toward the wafer's lower-left quadrant, watching the read-out approach those numbers; the mark sits on the street crossing nearest the flat's left end. The dicing lanes sit directly under the mark there, which is the point of putting it in a street but makes for a busy picture, so click the eye button on the Wafer row in the Layers tab to hide them; it becomes a crossed-out eye and that row's 58 shapes stop drawing. What is left is the mark, on both levels at once: the orange cross is the mark on Active, the clear-field level, and the blue hatched square around it is Metal1's dark-field window with a cross-shaped hole knocked out of it — both centred on the same coordinate, because they came from the same (x, y) in the same placement. The hairline running from the square's corner to the hole is the seam where that polygon closes; GDS boundaries have no hole primitive, so a hole is cut with a keyhole slit.

    Click either arm of the cross to check the size claim for yourself: the status bar picks up · 1 selected, the Properties panel reads W 100.00 µm, H 20.00 µm on layer Active (1/0), and the inline badges on the canvas say the same. That is the 100 µm cross, exactly as long as the street is wide.

    A close zoom on one alignment mark with the Wafer layer hidden: a blue hatched square with a plus-shaped hole knocked out of it, an orange hatched cross filling that hole exactly with its horizontal arm selected and carrying W 100.00 µm and 20.00 µm badges, a hairline seam from the square's lower-left corner to the hole, the Properties panel reading X -40900.00 µm, Y -40860.00 µm, W 100.00 µm, H 20.00 µm and Layer Active (1/0), the Wafer row in the Layers panel showing a crossed-out eye, and a toast reading Placed 6 marks (9 shapes) on 2 layers.

  13. Cross-check every level. Choose Verify → Check mark alignment…. This is read-only — it dispatches no command and touches nothing on the canvas. It expands every SREF/AREF instance in TOP first (so a mark buried inside a referenced cell on one level and drawn directly on another would still be compared), clusters small shapes per layer into candidate marks, then matches marks across layers within a tolerance. The report: Layers carrying mark-like shapes: 1/0, 2/0, Mark sites found: 3, and All 3 mark sites agree across every layer. No action needed. The 553 dies' own geometry never shows up as a false mark: the 4400 µm active square and the 1500 µm trace are both past the check's own max mark size 500 µm cutoff, which is stated in the report header beside the tolerance and the two cluster radii.

    Glyph's Mark alignment report for TOP: layers carrying mark-like shapes 1/0 and 2/0, mark sites found 3, scope the active cell with SREF/AREF instances expanded, tolerance 1 micrometre, match radius 50 micrometres, cluster radius 150 micrometres, max mark size 500 micrometres, and the result line reading All 3 mark sites agree across every layer, no action needed.

What you built

A 5 mm die drawn from a blank document — two layers, named and toned, a 4.4 mm active area and a metal trace, sized by typing rather than by dragging — then stepped into 553 copies across a 150 mm wafer as 26 AREFs and zero SREFs, in one undo entry, with dicing lanes derived straight from the 5.1 mm pitch and dies dropped wherever the primary flat or the 3 mm edge exclusion would clip them. On top of that, a three-site alignment-mark set in the scribe streets spanning a clear-field and a dark-field layer, placed in one more undo entry and confirmed, by a read-only geometric check, to agree at every site to within 1 µm. Close the report, un-hide the Wafer row and press Ctrl+0 to see all of it at once — at full-wafer scale the 100 µm marks are far below one pixel, which is the honest reason you cannot see them there.

Next steps

Read Arrange for the rest of the alignment, distribution and array toolkit that Wafer layout sits alongside, and Layers for how mask field tone (clear vs. dark) works and why it changes how a mark gets drawn. Design rule checking covers Glyph's other read-only Verify-menu check, run the same way as the mark-alignment report here. Then open the editor and step your own die across a wafer.

Updated 2026-08-25

Open Glyph — free, no install Your files never leave your computer.
Open Glyph →