here's two backyard mechanic methods.
1: A hammer, an old seatpost, and a vice.
Open up the vice an inch or so, lay the fender on it with the vice gap where you want your indent, hold the old seatpost like a baton on top, and beat it with a hammer till you get the indent you want.
Method B: big crescent wrench, little crescent wrench
Stick big crescent wrench in middle of area to be indented, and tighten it down snug.
Bend fender inwards with big crescent wrench. Bend a little further in than you need. Move big crescent wrench fore or aft and repeat til you have a dent slightly wider than you need.
Use little crescent wrench on both sides of your dent, twisting to make a square-ish transition from roundy fender to flat indent.
I can get factory looking indents using these barbaric methods, and do it all the time for fork clearance, and rear seat stay clearance.