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commercial cutting machines that will align to registration marks placed there with a printer

how to align our laser printer to registration marks

You need to do two things: Actually, I really like the pin-hole idea here. The jig would have pin-holes along the top side, and left side. The pins would be facing down (because the lasercutter bed has holes in it, the pins should be able to face downwards). This would allow you to skip the scanner step.