Few sights undermine confidence faster than layers that do not line up: the mask shifted from the copper, the silkscreen half a millimetre from its pads, or the whole drill pattern offset as a block. Understand this before touching anything: Gerbv draws each file in the coordinate space that file declares, so when layers misalign, the viewer is almost always reporting the truth — the files disagree. Misalignment is an export diagnosis, not a viewer setting. This guide explains the causes, how to use the drill layer to localise the disagreement, and how to fix the export so the set registers on its own. The normal stacking workflow is covered in load and align Gerber layers, which this guide assumes as the starting point, and current Gerbv builds are on the download page.
How misalignment presents
Read the pattern before reading the causes, because the pattern names the cause. A single layer shifted while all others agree points at that layer’s own export — a different origin, a mirrored output, or a stale file. All layers shifted together relative to the drill data, or drills shifted relative to all layers, points at two export runs that used different settings: typically the Gerber files exported in one session and the drill file in another. A shift that grows across the board — aligned in one corner, increasingly wrong toward the opposite corner — is not a shift at all but a scale disagreement, which means a format or unit difference between layers. A mirror image, where text reads backwards and asymmetric features swap sides, is a layer exported mirrored, usually a bottom layer produced with a mirror option intended for viewing rather than fabrication. Each pattern is fixed in a different place, so spend a minute classifying yours.
Cause 1: Layers exported with different origins
Every file must share one origin — one reference point for all coordinates. CAD tools let an export use the design origin, an absolute origin, or a user-placed origin, and if layers were plotted against different choices, they will be offset by the distance between those origins, everywhere, by the same amount. This happens most often when a set was not exported in one pass. The remedy is not to move anything in the viewer: re-export the entire set in one session, with one origin for every output, and reload.
Cause 2: Format and unit settings differ between layers
Gerber files declare their coordinate format and units inside the file, and the drill file declares its own. If layers were exported with different settings — one in millimetres, another in inches, or with different coordinate precision — the viewer honours each declaration and the stack disagrees, typically as a growing scale error rather than a clean shift. The full treatment of that signature is in millimetres vs inches, but the rule for this guide is the same: a scale-shaped misalignment is solved in the export settings, by giving every output — Gerber and Excellon alike — the same units and a compatible format, then re-exporting together. Check this cause especially when most layers came from one tool or preset and one file came from somewhere else, such as a drill file regenerated by a different utility.
Cause 3: Mixed revisions in one folder
The most human cause: the folder contains files from more than one export. A corrected top copper was copied in without removing the old one, so the stack shows a board arguing with its previous self. The tell is a small, design-like offset on one layer — a connector moved in the last edit — rather than a clean engineering offset. Clean the folder to one set from a single export, or extract the fabrication ZIP into a fresh folder and view that set instead.
Stepwise fix
- Isolate the disagreement. Show layers in pairs — copper with mask, copper with silkscreen, copper with drills — and identify exactly which file disagrees with the consensus of the others.
- Use the drill layer as reference. Load the Excellon file over the copper, as in viewing Excellon drill files. Holes must sit centred in pads across the whole board. Centred everywhere except one layer’s features confirms that layer as the outlier; holes offset from everything means the drill export used different settings.
- Check for mirroring. Read silkscreen text and compare an asymmetric feature on both sides. Backwards text on a fabrication layer means a mirrored export.
- Fix at the source. In your CAD tool, set one origin, one unit system and one format for all outputs, turn off any per-layer mirror that is not part of the fabrication intent, and re-export the complete set in one pass.
- Reload and re-verify. Open the fresh set, restack it, and repeat the drill-overlay check corner to corner before trusting it.
What not to do in the viewer
Do not nudge a layer into apparent alignment and then order from the original files — the factory receives the files, not your view, so a hand-aligned stack proves nothing and can hide a broken export behind a reassuring picture. Gerbv does have documented export operations that translate data for format-conversion work, but an inspection session is not the place to repair registration. If the set does not align as exported, it is not ready. Our measurement guide, measure distances in Gerbv, turns the residual question — aligned, but by how much where it matters — into numbers you can check against the design.
Prevention
Prevent misalignment by making re-export boring: one preset, one origin, one unit system, all outputs in one pass, into a clean folder, every time. Never assemble a send-set by copying individual files between export generations. And make the drill overlay the last check before any upload, because the drill layer — unambiguous, mechanical, impossible to argue with — will witness a registration problem that layer-to-layer eyeballing can miss.
Frequently asked questions
One layer is shifted but the rest align. What does that mean?
That layer was exported with different settings — a different origin, a mirror option, or it is a stale file from another revision. Re-export the complete set in one pass with one origin and one unit system, rather than adjusting anything in the viewer.
Why use the drill layer to check alignment?
Holes are unambiguous: every drill hit must sit centred in its pad on every copper layer it passes through, across the whole board. The drill overlay therefore localises which file disagrees with the rest.
Should I move a layer into place in Gerbv and order anyway?
No. The board house receives the files, not your adjusted view. A stack that only aligns after manual shifting is a broken export — fix the origin, units or mirroring in the CAD export and re-export the full set.