you need to make a determination here:
1) is this a radiused bottom nut slot? Fender and others use a radiused slot. for this case the bottom of the nut is radiused to match the slot radius. a nut blank can be purchased that has this radius pre-cut or you can scribe and file the radius on a flat bottom nut blank
2) is this a flat bottomed nut slot? if so, a nut slot file like StewMac sells works great to clean the slot - but you must practice your cleaning technique so that you don't rock the file while cleaning. rocking the file has the potential to create a slot with a hump in the middle
all the best,
R