Apply a positional tolerance to hole features is very straight forward in any CMM software:

but from time to time you'll positional tolerance applied on bolt hole pattern (a group of holes) in relationship to one datum only (typically the surface that these holes sit on). How this can be done correctly varies in different CMM software. In Open Dmis, just follow these steps:

1, Obviously you need to set your datum feature as your primary axis (level);

2, Then use the multiple points best fit option in co-ordinate tools:

What's important is you must constrain your DOF correctly, which in this simple case is allowing translation in both XY and rotation about Z only.

3, After your new best fit alignment done properly, re-apply your positional tolerance under new alignment:

This is your results of bolt hole pattern position to one single datum, but remember it is NOT necessarily better than previous results !