You probably have noticed that if you insert mold components (a quite decent component library is also supplied) with MTD that it will automatically drill the hole needed in all plates. That functions can be used for other stuff, so check the the function called "drill component.."
I have seen demonstrations made with this function that are quite interesting, the example I saw was using a catalog with standard part, this case ball bearings, after the ball bearing was positioned this function was called and it removed material on a housing to seat the ball bearing. Looking closer on the ball bearing part I noticed that it used negative solid with predefined naming what this function used. In the same demonstation they inserted a key on an axle and after this function we could see a slightly oversized hole in the length direction according to the std.
maybe helpful?