If you play with embedded electronics long enough, you will eventually need to enclose your project. For some people (like me!), cutting and sawing on an enclosure seems daunting compared to designing an electronic widget. Seems silly doesn't it? To ease our fears, Casey has written a great tutorial on simple enclosure modification. 
When I've modified enclosures, I make a drawing, double-check everything, then use a metal scribe to make the marks on the plastic. Then I cut them out with a jeweler's saw, cutting a bit inside the lines, and use a file for the final fitting. It could be done quicker, but it gives me good results. The key is to make the first cuts inside where you calculated, so if you're off by a millimeter or two you don't end up with ugly gaps.
Keith
When I started modding enclosures, I first used masking tape over the area and then just drew my template on that. The idea being that the tape would protect the plastic surface.
Now, I print them to a label and then apply the label template to the side I am going to cut. You can then use a utility knife to score the cuts.
For connectors like D-Subs, drill your screw holes first, then cut the bulk.
Thanks for the info (by email) that the white markings on the enclosure were made with a "grease pencil" from a craft or artist supply store, and the marks can be wiped away using alcohol or warm water.
At my local Michael's I was able to find a grease pencil, though the packaging didn't actually use that phrase. I found the "Scribe-All All Surface Pencils" from General Pencil Co.