If the fender is not actually deformed, I just do what you can with the stays. On a bike with horizontal dropouts it may be nearly impossible.

If the plastic is really deformed, and it's really all plastic (no metal core?) then moderate heat will soften the material enough that you can correct some problems. I think a heat gun would be overkill, though. I have had some success using a sink full of very hot water; correct the bend with your fingers while keeping the water hot... as hot as you can stand.

I have a pair of black plastic Zefal fenders that have a metal core similar to the old ESGE and new SKS Chromoplast fenders. Heat won't do any good with those, but you can bend them by hand. Is the overall radius of the fender correct? If you make a fender wider, you will reduce the radius. If you narrow it, you increase the radius.