You can have Best Fit Alignments solve 2D, 3D, or custom user-defined degrees of freedom. Some important differences between these best fit alignment types are:
A 2D Best Fit alignment requires an initial alignment to establish the 2D plane. The alignment is created in the workplane defined by the current active alignment.
A 3D Best Fit alignment uses the raw (machine) data and correlates it to the theoretical values. It does not require a previous alignment, but if the degrees of freedom are set to rotation-only and a rotation center is not explicitly defined, it uses the origin of the current active alignment as the rotation center.
In most cases, a user-defined Best Fit alignment requires a previous alignment in order to reliably establish the XYZ directions for the custom degrees of freedom.