Methods and systems are provided for manufacturing an appliance for correcting malocclusions of a patient's teeth. The method may include measuring the positions of a patient's teeth and receiving tooth movement constraints. The method may also include generating an initial treatment plan based on the measured tooth positions and the tooth movement constraints and measuring the malocclusions of the patient's teeth for one or more types of dental malocclusions. The method may also include generating a plurality of treatment plans from the initial treatment plan based on the measured malocclusion and generating a model of an appliance for each stage of the treatment plan. The method may also include generating instructions for fabricating the appliance for each stage of the treatment plan based on the model of the appliance for each stage of the treatment plan.