I use MoI to design parts for 3D printing - Everything from fixtures to electronic enclosures to CNC machine components. Clearance is a big consideration as nobody likes having to drill or file parts to make them fit.

For bolt holes and heat-set brass inserts I use the method described by Barry above - That is, an object library of pre-defined "hole cutters".

For parts that fit together (example: a stepper motor boss fitting into a bracket hole) I normally enlarge the part (the motor) slightly by resizing it, perform the Boolean diff operation, then re-size the part back to its nominal dimensions. It would be cool to have a short cut key you could press just prior to a Boolean diff that would enlarge the resulting opening by a predefined clearance distance.

Ed Ferguson