Starting with the appropriate (English, French, Italian) cotters, I do an initial assessment of how much I need to file by seating the cotter in the crankarm/bb assembly. Depending on how much protrudes, I resolve to file more or less.

I use a large (12") good quality Mill file with a bastard cut (excuse my language! ) and a bench vise with good square jaws, such as will allow a good grip on the cotter.

My objective is to effect a completely flat face, maintaining the same angle as was extant on the cotter from the manufacturer. This will yield full faced contact to the bb, and maintain alignment of the crank arms to each other.

I try err on the conservative side filing less rather than too much, but generally going back at it with the file a second time is where I mess up, in which case I have to start over with a new cotter.

After you mess up a lot, you'll get better at it too.