An orthodontic appliance is automatically designed and manufactured from digital lower jaw and tooth shape data of a patient. A computer calculates the post-treatment positions of the teeth and produces three-dimensional images of the teeth, individually and in their calculated positions. 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 doctors changes. Brackets are fabricated as an integrated set, either by cutting slots therein or by building the brackets in layers by, for example, stereo lithography. Three-dimensional custom jigs are automatically made to exactly position the brackets on a patients teeth.