apekim,
If you want to be formal, you can prepare an Altered Item Drawing. Specify the MS part number and the appropriate black oxide coating process for the part's material (such as MIL-DTL-13924, class 4 for 300 series cres) on the drawing.
The altered part should then be assigned a new part number.
Black oxide coating is only cosmetic in nature and does not provide corrosion protection. That is why it is not widely used in aerospace.
Hope that helped.
Terry