HSM Express+Tormach undersized holes

[billbo911]

OK, next rookie question.

When milling this part, the wall thickness is approximately/ideally .125".



The pocket comes out as expected. The problem is the bearing holes. They will usually have what amounts to a layer of aluminum foil at the bottom.

Here is what I am thinking should be done to prevent this, so please feel free to correct me.

1) Mill this in two separate processes. One for the pocket, one for the holes.
2) On the process for the holes, offset the Z zero by a few thousandths.

What process, or steps would you perform to prevent this?

(Just in case you are wondering, this part is literally just for the sake of learning and has no other purpose.)

EDIT
I just found a simple answer, "Bottom Height Offset".
Set it to something like -.01" and you get a nice extension of the bit past the end of the hole, and a clean edge.