Make sure all the bottom edges of the canopy are supported when cutting. Make sure the plastic is not bent or under any kind of stress while cutting.
Use an abrasive cutoff wheel. A wheel made to cut steel works great. Make sure the wheel is balanced. One wants smooth cutting. I use an angle grinder and a 5-inch wheel. A dremel tool or air tool also works well, just not as fast.
Don't use a jigsaw. Don't use any kind of tool that isn't smooth.
Sometimes a canopy has to be bent to get it to fit its frame. In this case, bend the canopy, mark where you need to drill, let the canopy relax, then drill the hole. Make sure the holes are larger than the rivet, screw, or bolt you are putting through it. How much larger? Enough so nothing binds.
Todd