A method by which an orthodontic appliance is automatically designed and manufactured from digital lower jaw and tooth shape data of a patient provides for the scanning of the mouth of a patient to produce a three-dimensional digitized model of the shapes of the patient's teeth and their positions in the patient's mouth. The appliance is automatically designed according to the final design, which also can be interactively modified and approved by the orthodontist, with the computer recalculating the effects on the treatment as a result of the doctor's changes. Brackets are fabricated as an integrated set, either by cutting slots therein or by building the brackets in layers. Three-dimensional custom jigs are automatically made to exactly position the brackets on a patient's teeth.