I rarely find the existing windows good enough to use as templates so I will use them as a guide only to make a perfect routing template out of 1/4" Masonite, I use this to mark the cast acrylic or polycarbonate, i then cut it out close to the line on the bandsaw, but a good jigsaw with a plastics blade works fine too, I then flush rout it to the template with a spiral downcut bit, sand out any chatter marks with 180grit dry and then a final polish with 00 steel wool.I don't go the extra step of flame polishing because I don't want the super clear look and also according to the local acrylic company who make all sorts of products out of acrylic or polycarbonate it is one of the causes, along with solvents and window cleaners etc that speed up the inevitable internal crazing in acrylic.
Steve.