Don't file the axle. The last thing you want is to weaken it. I'd file the dropouts working on the same face (front OR rear) on both sides of the fork and stop as soon as the axle fits. Also, dont file the top of the dropout as you don't want the wheel "cocked" vertically either.

I just realized this is a double post and FBinNY gave the same advice I did on the other thread.