I use a band saw to chop up my boards.
but still ended up with pin holes and crap. Here the reason was I used an ink jet transparency that clearly wasn't opaque enough.
I use a laser printer for mine and I've never had any real trouble with it. Occasionally it wont put toner down in a tiny area, creating, as you've mentioned a pin hole, but usually there's only one per design and usually this isn't in a critical area.
Back in high school I took the electronics course, and as part of that we had to build a simple project, this included making a PCB. To help with the pin hole issue we put the transparency through the printer twice, thus doubling up the thickness of the ink layer. The printer used here was a laser too.
I have tried doing this myself and it doesn't work, the transparency doesn't align itself well enough to print over the exact same area. With small SMD packages this is completely unacceptable, the spacing I use between 0.5 pitch pins is only 0.228mm, so there's no margin for error.
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