Put the tire in full compression in the driveway. Take a felt pen and trace a line say 1" all around the tire. Some guys cut to the line with a recipe saw. I used a grinder, metal cutting wheel. I then used the cut piece to trace a line on the opposite side. You will be limited at the front by the body structure but the main concern is for vertical travel.
Before you start trace a line around the outside of your flare. Make sure to stay inside that line. AND measure up inside the wheel tub. You don't want to cut past the wheel well either.
Grind, polish, smooth the cut edge and if you are anal like me you could use a body hammer / dolly to fold the edge in. A bit stronger and a nicer finish... like the factory edge was. Then prime/paint etc.
The only area which really needs trimming is the rear edge. It is possible to get all the clearance you need just trimming that back edge. But still make the marks by tracing a line with the tire fully stuffed.