Here is the Tutorial for the geometry modeler from ANSYS WORKBENCH.

To get to this, OPEN WORKBENCH, the select NEW GEOMETRY to start the DESIGN_MODELER_8.1. Then select HELP from the menu at the top. Read from the beginning and about 5 windows in (the arrows) you will be at this page. Here is the menu location of this tutorial. If you work through this example, you will use all the tools you need to make holes or cut off corners etc from your extruded parts.

This tutorial makes the holes by extruding them from the beginning. To make holes after the fact, see below.

Go to the help, enter search on BOOLEAN and choose BOOLEAN OPERATIONS. The CUT MATERIAL is the one to use. You can also use the SLICE material when all bodies are frozen. To make a hole in something, Create the intersecting geometry, then use BODY OPERATION CUT MATERIAL and select the pieces you want to cut away. The object you are cutting from must be unfrozen. Take a look at the next page for example to see a cut in a pipe. The cylinders were cut from the hollow pipe. Interestingly, even though the cylinder started at the xy plane, the cut did not go all the way through. Apparently the cutting object must completely pass through the object from which the material is removed, necessitating a new plane be built to shift the objects. Feel free to click around to remove some material.

See that two cylinders that were extruded from the XY plane into the Z direction by 12 inches were removed. When I hit generate, the cylinders that were here disappeared, along with the holes in the pipe. If the cylinders had been longer (into the negative Z side), I would have clearance holes through the pipe.