1. A method for determining appliance geometries for orthodontic treatment of a patient's masticatory system, the method comprising: generating, with aid of a processor, a computer representation of the masticatory system of the patient; determining, with aid of the processor, an arch curve corresponding to a desired arrangement for a set of teeth of the masticatory system; digitally modelling, with aid of the processor, the set of teeth in a plurality of different arrangements representing successive repositioning of the set of teeth from an initial arrangement toward the desired arrangement; and generating, with aid of the processor, a plurality of appliances corresponding to the plurality of different arrangements, the plurality of appliances each having teeth receiving cavities, wherein the teeth receiving cavities of successive appliances have different geometries shaped to receive and resiliently reposition the set of teeth from one arrangement to a successive arrangement, and wherein the plurality of appliances is generated prior to the patient wearing an appliance of the plurality so as to reposition the set of teeth.