Is the Yugoslav Ju-52 in there hehe
Tape the cut lines to prevent damage from any slips, then mark the actual cut lines on the tape with a thin pencil. Use a thin-blade razor saw, and make each cut carefully and slowly. I'd need to see the actual panel to advise on the sequence, but, as the 'removed' panel is likely to be discarded and replaced with thinner, clear sheet, if necessary, diagonal cuts from corner to corner may simplify the process, and the problem of cutting at 90 degrees from the first cut.
If you can post a clear shot of the canopy part, and one with the area to be removed marked out, I can possibly explain better. I'm planning on doing this on my He111 canopy roof panel, but it can be done from the rear edge for each fore and aft cut, so a little easier.