You can file slots with strings, but dont use deep slots in the nut. It will cause the strings to bind when tuning and you'll end up in a worse place.
The string in the slot should be at about 2/3 the string depth.
If the nut is too tall after getting the slots right, then take some off the top of the nut to effectively make the slots shallower and the nut not as tall.
See here:
http://www.stewmac.com/How-To/Online...lot_Depth.html