Do you have to extract the geometry from an imported file to machine it?

Using the Profiler is a generally cleaner solution. However, profiler doesn't always solve every task. Sometimes extracting geometry is necessary, especially if you need to tweak geometry.

The reason I was asking is I had a pocket with an angle leading into it on one end and had problems generating a good program. It kept wanting to cut into the sides. I was wondering if I would have extracted the geometry if it would have worked.