A multiple-stage treatment method of orthodontically correcting teeth of a patient. The patient may wear, during the night and whenever convenient, a tooth positioner shaped to fit their dentition. The patient may then wear, at other times, an arch aligner shaped to fit their dentition. The patient may progress in stages, with the patient using a different arch aligner at every stage and a different tooth positioner every several stages. The combination of the arch aligner and tooth positioner may be used to treat, among other problems, class II and class III malocclusions, or transverse or vertical malocclusions, while maximizing the potential for patient compliance and reducing the number of tooth positioners and/or arch aligners that have to be made.