The 2D and 3D options tell PC-DMIS whether to construct the feature as a 2D or 3D ellipse. These options become available if you select the Best Fit or BF Recomp option.
If you select 2D, PC-DMIS constructs the ellipse, projecting it onto the workplane.
If you select 3D, PC-DMIS constructs a best fit plane from the inputs. Those inputs are then projected to the plane, and a constructed ellipse is created from the projected points.