create your clamps as solids (or wire frame) entitees ..insert them and then define them as stock ... make sure to define them oversize so your cutter has a little clearance.use update fixtures (m functions)to add them to the seq.
when roughing click on the fixtures (clamps) as well as the part geometry.
when you are ready run the simulater. save the part you have cut as an stl
and then re insert it into your part program... do a rest roughing and select the model you inserted and then it will machine all the material away where there used to be clamps (make sure to update your clamp/fixtures again )