a) file only one side; if rear, file the bottom side. This is so you keep the side the axle will bear on the same. If you're good enough to file all four surfaces and have them flat, square, and aligned then you don't need to read this.

b) mount the frame/fork so you have the flat of the side you are going to file parallel with another flat reflective surface. The surface has to be shiny and flat enough that you can compare the sheen you make as you file with the reference surface. I use the top face of the vice jaws. This helps you make a single flat across the whole dropout face, hopefully parallel..

c) check with a bare axle as you file - not just for go/no-go, but also for alignment (axle needs to be 90 degrees to the dropouts when you have filed BOTH of them).

d) go slowly, check often.


Of course it helps if you know how to use a file, which one for which part of the job, and have done this before.