Originally Posted by
Gavin1393
Have a look at the nut slot depths, make sure that they follow the 12" radius (or in english) that they are much the same height above the fretboard.
If this is the case, rather than having some slots deeper than others which will lead to buzzing if reduced further, then proceed as Wokka suggested and work from the flat bottom of the nut. When sanding the nut, plastic or bone, you should use sandpaper attached to a known flat surface. You want the nut to have as much contact as possible with the neck slot. Stability and sound transfer.
I'm assuming you haven't done a fret levelling job on the guitar? But not an issue except if you are going for a very low action, hence you should check the curvature of the fretboard and neck with a (notched) straight edge or long ruler. This is an important starting point to getting your action and intonation right.