How do I measure the best-fit plane through a molecule?

You can calculate the best-fit lattice plane through three or more selected atoms, using the Calculate > Plane Through Points command. Details of the fit results are displayed in the window log.

If you are working with a crystal, a lattice plane will be shown passing through the selected atoms. If, on the other hand, you are dealing with an isolated group of atoms (i.e., in "molecule mode"), then a lattice plane cannot be shown because there is no unit cell. If you wish to show a plane you can either:

Measure Inter-Planar Angle

Measure Inter-Molecular Angle