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I've been trying to convert DXF/Gerber file to NC Drill file.

Thanks for sending a sample file.  To create Drill data, FAB 3000 requires Flashed data.  Why?  Because a flash contains a center point and diameter which is then used to create each Drill Hit.  

1.  During DXF import, the easiest way to create flashed data is Check the layer option "Flash; and the drill holes should be drawn in your DXF using the entity: Circle.  Then go to Step #2.

Note:  In your DXF they are drawn twice:  once as a Polyline (with multiple sides - think of an octagon) on layer BOTTOM, and then a Hatch filled entity on Layer 0.   So you will have to perform an extra step after DXF import to convert those polylines to flashes.   You'll need to use the Command "Draw to Flash" (menu:  Tools | Draw to Flash | Automatic).

2.  Convert Gerber Layer to Drill  (menu:  Tools | Drill | Gerber Layer to Drill...).   The command takes all Flashed data on your selected layer and converts it to Drill data using the center point and diameter of each Flash to create the drill hit.

3. Export Drill Data.  Go to menu:  File | Export | Drill...

Here's a quick tutorial (including the extra steps you'll need to take):
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