Techniques for preparing a model (e.g., a digital model) of a person's teeth are described. The techniques include receiving a model of a maxillary arch and a mandibular arch of a person's teeth, operating an automated mesh cleaning operation to modify the model, segmenting the model to identify individual teeth and gum tissue in the model, identifying and marking features of each tooth of the model, and adjusting the individual teeth of the model into a recommended orientation relative to each other, and applying a treatment method. The treatment method may include a selection of a bracket type and an aligner type. The techniques may determine a proposed location of brackets or aligners on the individual teeth based on the applied treatment method and export a digital model of a bracket tray for formation of a bracket tray that can be used to secure the brackets to a person's teeth.