What Was Supposed to Happen
To start, you must first cut a piece of stock of your choice material to the appropriate size. For this piece, wax is the most appropriate material, as it is easy to cut, and the functionality of the part does not require anything stronger (ie plastic). 

From there, you put the stock into the CNC machine, and run it with the appropriate file. 

What is the appropriate file?

take the .igs file from Iron CAD and import it into ProE. Once in ProE the file can be edited for manufacturing by the milling machine.

What Actually Happened
We were able to cut the block of wax with the milling machine, down to our specified size. However, the file was missing some information, and ill-formatted. It was two dimensional almost isometric like an envelope instead of a three dimensional solid. When we tried to tell it to cut things out it couldn't because you can't cut things out of something that isn't a solid.

Alternatives? 

The alternative is to use the milling machine to manually put in the holes and divots with the appropriate drill bits. This can be done using the coordinate system on the milling machine. To do this, you must center the drill bit on a corner of the stock, and then turn on the coordinates, setting that point to (0,0). From there, the appropriate cuts can be made from a printed CAD file that has the measurements of where to put the holes.

Why didn't we do this?

The estimated time for this method is one day of work. Being in the midst of midterms, this was not a possibility for our group. Nor would this be very fair to our group, being that other groups worked 2-4 hours. We had already put in about two hours figuring out the stock, and an additional (estimated) eight hours was not extremely feasible.

What We Would Do Differently
We would somehow procure the appropriate file to work with, whether it be through wining, or perhaps paying a senior mechanical engineer to help us with it.