For my nuts, I usually tilt the file to be parallel with the face of the peghead, and just file down the slot until it's low enough. Then maybe a couple swipes parallel with the fretboard to round the slots over so the string have a gentle curve from the peghead to the fretboard.
There's a video I watched from Robbie O'Brien on the subject, I suggest you look it up. I think it's something about guitar set up, or maybe intonation. (No affiliation/interest)
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