1. A method for automated detection of deviations from an orthodontic treatment plan, comprising: receiving a tracking model comprising a digital representation of an actual arrangement of a patient's teeth after an orthodontic treatment plan has begun for the patient for comparison to a plan model comprising a pre-determined planned arrangement of the patient's teeth; performing an automatic matching step between teeth in the plan model and the tracking model such that teeth in the plan model are repositioned to substantially match corresponding tooth positions in the tracking model; comparing the tracking model with the plan model so as to detect stationary elements of the patient's dentition such that positions of one or more non-stationary teeth are measurable relative to the detected stationary elements; measuring achieved tooth movements in the tracking model; and detecting one or more positional differences between the actual arrangement of the patient's teeth and the pre-determined planned arrangement of the patient's teeth.