1. A method of identifying deviations from an orthodontic treatment plan, comprising: receiving, on a computer, an unsegmented three dimensional (3-D) digital representation of an actual arrangement of a patient's teeth after an orthodontic treatment plan has begun for the patient and prior to completion of the orthodontic treatment plan; and comparing, using a computer, the actual arrangement 3-D digital representation to a previously segmented 3-D digital model of a pre-determined planned arrangement to determine if the actual arrangement substantially deviates from the planned arrangement, the comparing comprising matching a surface of a tooth from the previously segmented, planned arrangement 3-D model to a surface of the unsegmented 3-D digital representation of the actual arrangement; and calculating one or more positional differences between the actual and planned arrangements of at least some of the corresponding teeth based on the surface matching; wherein positional parameters examined include tooth rotation, extrusion, intrusion, angulation, inclination, and translation.