A method for treating a subject's teeth. A target configuration for the subject's teeth is determined. Receiving features are produced on a dental base in response to the target configuration, the receiving features being configured to receive physical tooth models. The physical tooth models are assembled on the dental base to form a physical arch model. A dental aligner is produced using the physical arch model to move the subject's teeth to the target configuration. A method for making a multi-layer dental aligner includes placing a first layer of a first aligner-making material over one or more physical tooth models, conforming the first layer of the first aligner-making material to the surfaces of the one or more physical tooth models, placing a second layer of a second aligner-making material over the first layer of the first aligner-making material, and conforming the second layer of the second aligner-making material to the surfaces of the first layer of the first aligner-making material over the one or more physical tooth models to produce the multi-layer dental aligner. A method for making a non-uniform dental aligner includes non-uniformly heating the sheet of aligner-making material and holding the sheet of aligner-making material against one or more physical tooth models to produce the non-uniform dental aligner.
