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We are using FAB3000 to compare layer for overlapping between layer.

There are several methods available to find and compare any differences between layers.

After loading all layers into FAB 3000 (i.e import Gerber, ODB++, 2581, etc.), use the command Compare Layers. Menu: Tools / Compare Jobs and Layers / Compare Jobs and Layers / Compare Jobs...

Important: Make sure to set the error tolerance size to 1 mil (0.0254 mm) or less.  The default value set is 2.5 mil (0.063mm) which does not produce the best values.

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