Methods for designing orthodontic appliances are provided. In some embodiments, a method includes receiving a treatment plan for a patient's dentition and generating an aligner model representing an aligner configured to implement a treatment stage of the treatment plan. The aligner model can include a thickness map having a thickness parameter for each location of the aligner model. The method can include adjusting the thickness map by using the aligner model to evaluate an outcome when the aligner is applied to the patient's dentition, and iteratively reducing the value of each thickness parameter of the thickness map based on the evaluation until a resulting thickness is determined for each thickness parameter. The method can also include providing instructions to manufacture the aligner based on the aligner model with the resulting thickness for each thickness parameter of the thickness map.