I have done that very thing. Filing on a Ruger I mean. Generally, Rugers shoot to point of aim with the standard weight bullet for that caliber. Shoot lighter bullets and usually get lower groups. What I do (may not the best thing for you) is develop the load I want, and then file if needed. I use small hobby files so not to take off too much or leave gouges. Then when I have it the right height, I use a smooth sharpening stone and emery cloth to polish it smooth. If it's a blued sight, be careful not to touch the flat side that faces you.
The last gun I filed was a Charter Arms. The 200 grain factory rounds I wanted to carry shot way low, so I took the gun and the files to the range and commenced adjusting by filing, shooting, and repeating until I was dead center at 20 yards. You can even file the front sight for windage, but turns out untidy.
You can even file the front sight for windage, but most guns don't lend themselves to that without the end result looking untidy. Let's say you wanted the front sight moved to the right; just take some off the right side of the front blade, then to center in the rear notch, you'd have to pull the front end a little closer that way.