Brass, being (fairly) soft, and a hundred to do might persuade me to make a cutter to fit on a counter-bore which fits the hole precisely. I expect it depends on the quality of the tool, if purchasing.
If any are very slightly proud (the odd thou or two, not much more) and it is required flat, the parts may be ‘flatted’ afterwards? Face mill, horizontal slab milling cutter, fly cutter, surface grinder – even a linisher – are all options that may be available/appropriate.