There is a "correct" height for nut slots - since good intonation is considered correct the nut should behave like a fret. That's how high the slots should be - and I agree with Redir, it's just slow and careful one slot at a time. We're removing small fractions of millimetres until it's right.
If someone wants a higher but well intonated first position then a compensated nut is for them.
I can see instantly if a guitar has been set up by a competent tech prior to me getting it, or not since leaving the factory .. and sometimes if the owner has had a go at it first.
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