Typically, you would use a collet (a multi-jaw chuck or other such device) to close down around the cylindrical datum feature. The centre axis of the collet simulates the datum axis of the cylindrical feature. If you don't want to use this method, you can take two groups of three points (prefer 7 & 11 pts to minimize lobing effects) to generate two circles, resulting in one common datum axis. Not a great way to do it, but useful if a taper is present. Personally, I'm always concerned about how well the generated axis represents the real one, but that's a decision for you. This is a fairly advanced topic as far inspection is concerned, so be careful using the two circles to generate the datum. Hope it helps.
Jim Sykes, P.Eng, GDTP-S
Profile Services
CAD-Documentation-GD&T-Product Development