Lots of folks are 3D printing prototype enclosures these days–if you search the forum a number of folks have done that for Spark projects.
For prototype plastic boxes, I have used an exacto knife blade bolted a soldering iron as a hot knife to cut openings in plastic cases–it leaves a cleaner but sometimes rolled up edge. You have to experiment to find the right speed to melt through.
For small scale production, I have used a local machinist and got him to mill them on a milling maching. Later I bought a milling machine and have done it myself. You have to experiment a bit since the plastic wants to weld itself to the cutter if you go too fast. Sometimes using a special bit with different cutting angle designed for plastic works better. I got my tabletop milling machine from Little Machine Shop but there are lots of suppliers including old machinery.
Last time I had to do a production runs of a few thousand plastic boxes, I got the box maker to machine them for me. I also got them nickel sprayed on the inside for RFI shielding but it depends on your antenna configuration.