Actually you are not permitted to remove material from the flange, at least by ASME B16.5-2003 or CSA Z245.12-05. Addition of material is permitted up to 1/16 inch, i.e. weld repair of the raised face, but taking away mass is strictly forbidden.
Think about it, would you not be changing the rating of the flange by reducing its mass?
Kenneth J Hueston, PEng
Principal
Sturni-Hueston Engineering Inc
Edmonton, Alberta Canada