1. A computer-implemented method for managing a patient's progression through an orthodontic treatment plan, comprising: detecting, using a computer, a deviation of an actual arrangement of a patient's teeth from a planned arrangement of the orthodontic treatment plan, wherein the deviation is detected by comparing a previously segmented digital three-dimensional (3D) model of the planned arrangement to an unsegmented 3D digital representation of the actual arrangement; and generating, using a computer, instructions for fabricating at least one orthodontic appliance configured to correct the deviation.