In the following, see two examples of polygonal cut-outs. First, a normal poly-cut and second, a cut-out using a solid whose intersection is subtracted.

Create a Penetration

Example of creating a penetration with tubes:

Select in the Polycuts options.

Select the large tube, then one of the small tubes in that order to cut out its volume. Select the large tube again and then the other small tube, in that order to cut out its volume.