As I said it is in your technique, believe it or not filing is an art if done properly.
As an apprentice I thought my foreman was the biggest barstard unhung when he made us file a square block to fit in a square hole with no more than .002" clearance.
As a tradesman 40 years later he was a barstard but it taught me how to file properly.
What you do is get the file closest to the particular gauge you are using and cut to depth using a depth set such as feeler gauges stacked up on the fret board to give the proper height.
For width cut in a figure 8 motion, you need a small clearance, a few thou' will do, you have a good leeway as you can usually go up from .009 to .011 without having to widen.
One other thing, don't have the cut too deep. By that I mean the depth should be shallow, if it is too deep it will be able to bind on the sides, the depth usually reckoned to be best is just over half the diameter of the string, all it has to do is locate and stop it popping out.
Have a go but it's hard to put back once you have removed it.
Go slowly, and remember that most guitar repair people get 70% - 90% of our repairs from people who have tried to do it themselves without putting a lot of thought in first.