Ok, So i know that I said that Alinspired's method stopped working, but I stepped away from my computer for a few hours and then went back and the method started working again. So, I got all of my holes cut out by projecting the curve onto the surface.

NOW, my issue is that when I go to convert the NURBS to POLYGONS the geometry that I get causes multiple points and faces that are making the object very difficult to work with. If anyone knows how to convert it without these issues please let me know!

All advice is welcome
Jenni

PS. David, thank you very much for the tutorial on the transparency, it was very helpful!