It is very common for the drill files to not align with gerber files (many PCB CAD software using different origins when exporting their gerbers & drills). Fortunately FAB 3000 can perform the alignment for you. Please perform the following:
Once you have imported your manufacturing data into FAB 3000, please perform the following to align any layer:
Go to menu: Edit / Align Layers
Select a reference object on the "Base Layer" (i.e Good Layer).
Now Select the similar reference object on the Layer to be Aligned. The layer is instantly Aligned.
Repeat Step #3 for any other layer that needs to be aligned.
Here's a tutorial movie showing the steps:
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