Perform basic shape operations early so that the net shape is attained while the number of surfaces is limited. Extra material only means that subsequent operations may look for more unnecessary intersections. As a result, the total CPU time will be reduced. Many solid modeling programs today provide "localized" operations. Use them when available to help minimize this concern.
Source:
Dr. Richard Lowrey, Mechanical Engineering Consultant
Don LaCourse, Principal Partner, eDocHelp