1. Verify PDF Import Options
MAP LAYERS: "Separate Color per Layer"
Note: This allows FAB 3000 to create separate layers for each object color
CONVERT PATHS to: "Rounded Path"
Note: Since you have a PCB, traces & silkscreen are typically expected to be rounded paths - when possible.
2. Load PDF into FAB 3000.
Note: Since FAB 3000 is a full-featured editor you can perform the following:
A. Rename Layers
B. Create Drill Tools.
C. Convert Circles to Flashed pads.
Why? Most PCB manufacturers like having "Flashes" for circular pads in their Gerber files.
D. Merge Trace and Pad layers.
3. Export to Gerber and drill.
You can obviously use many more advanced features of FAB 3000 such as panelize, DFM check, etc.