Of course you can do it, but most are finished pretty good already, whats important is contact footprint, is the heat sink sitting perfectly flat and not cocked, making excellent contact with the GPU die.
And also no excessive thermal compound, just enough to fill the voids and that's a very small amount, usually trial fitting and checking the results is the best way to determine good contact.
If you lapp a GPU heat sink you need to know exactly what you're doing, and you having to ask this question already shows you don't.