1. A system for planning an orthodontic treatment of a patient's teeth, the system comprising: at least one processor; a display device coupled to the at least one processor; and a data storage device coupled to at least one processor, the data storage device storing program instructions that when executed causes the at least one processor to: receive an initial position digital data set representing an arrangement of the patient's teeth; generate a final position digital data set representing the patient's teeth in a desired or prescribed arrangement; and generate a plurality of intermediate digital data sets representing intermediate arrangements of the patient's teeth, wherein at least some of the intermediate tooth arrangements represent different orthodontic treatment stages as the patient's teeth are moved from the initial arrangement toward the final arrangement.