I usually use a triangle file to do the filing, that way i can file all the way up to the tight corner of the sight. When you are filing remember that it's easier to take more metal off than it is to put metal on. Also remember it's better to make an error on the less expensive part, which is why the sight is filed and not the cut-out on the slide. When you are filing you want to maintain the same angle of the sight.
In this photo you can see where the rear sights were filed from the factory. You can also see that on the sight on the left there is some remaining Loctite that the factory used. The sight on the left is from my EMP and the sight on the right is from my TRP.
I file just enough so that the sight can start onto the dovetail about 1/3 of the way on, then i finish with a sight pusher. I've been using a B&J Machine P500 sight pusher for about 10 years now. One thing that I'm doing differently with it is I use the square pin in-between the round pin when installing sights. The reason is that the tips are worn and turn with the screw which could leave a mark on the new sight.
I use a B&J Machine P500 sight tool that you can get from Brownell's
I use a caliper to see that the sight is centered on the slide, which hasn't failed me yet. Once centered, I'll place a drop of blue Loctite on the set screw to keep it from loosening up. This is just an extra precaution even though I like to fit the sight really tight to the slide.
Here's what the final product looks like: