I just cut one of my front fenders last night. Like yellow75, I used my rotozip with the cutoff wheel. Cuts like butter.
Hold the flare in the position you want and mark. I'm using stainless steel screws on mine so I put the flare on with three screws and marked it. Then use 1 inch masking tape, preferably the blue stuff (it comes off easier), and tape along the mark line such that the bottom edge of tape becomes your cut line. Then cut and be careful.
With the rotozip, I make an initial pass but not cut all the way through. Then the second pass goes through.
You can use the wheel to smooth the cut too. A little rustoleum will help guard that fresh metal from suface rust too. Good luck.