Computer-based techniques are described that use orthodontic prescription templates to assist an orthodontic practitioner in creating a patient-specific orthodontic prescription. In particular, an orthodontic practitioner may retrieve a stored electronic orthodontic prescription template. The practitioner may then generate an orthodontic prescription that is specific to a patient's teeth by modifying one or more bracket attributes of the template within orthodontic modeling software. Subsequently, the practitioner may communicate the patient-specific orthodontic prescription to a manufacturing facility that constructs an indirect bonding tray for use in physically placing brackets on the patient's teeth.