don't see anywhere written anything about what you usin'.. nurbs.. poly..
i'm guessin' poly cause you mentioned square holes..
if it's nurbs you can trim away.. otherwize if it's poly.. you can make a poly cylinder and use the boolean tool (located in the Polygon menu..) select your model and then the cylinder and perform a Difference.. the cylinder should dissapear along with the part on the model it was intersecting with.. just remember to delete history each time you use the boolean..
:p