Clearing material above drilled holes

Kiri:Moto CAM
1

Any advice for clearing the area over my drill holes? The pocketing operation is going around the holes and leaving weird raised areas. I wonder if I just make two cut files to get around this, the first without the holes and without the drill operation. Then a second pass to add the holes.

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2

you can use a trace operation to select the holes then select “type → clear”