There are two immediate way i can think of. try this first,
1. create a block with 4x4x4. Using select surface mode, hit just the centre 4 surfaces.
2. In the surface menu, select Divide.
3. This will give you the more surfaces you need to play around with. You can also asdjust the vertices to suit your shape if you wish!
4.Then again in surface select mode, just select the individual surfaces you want to delete.
5. And boom you have you own holes where ever and whenever you need them!
