Thanks very much everyone.
First of all, yep--I meant the GTP layer, not GTS. That was my mistake

Second, I was considering cutting it by hand with an X-ACTO knife, though I was a bit concerned about the pads on the QFN package. They are extremely fine, as you can see in the attached image.
Unfortunately I do not currently have access to a laser cutter, so I am working at very low volume for now. In the past I have always hand-soldered my SMD boards, but that's not really an option now that I am using a QFN. The idea was to print out an actual-size image of the paste layer, tape it to the Kapton, then cut through the paper and the Kapton together. Again, that will still be difficult to do for the micro pins.
Your suggestions are appreciated!
Matt