A system and method for orthodontic alignment includes a radiographic template. The radiographic template has a plurality of metallic markers. A negative impression of a patients dental arch is made. At least one orthodontic treatment aligner is produced. The aligner is manufactured based in part on a computed axial tomography (CT) scan of a patient wearing the radiographic template and a separate scan of the radiographic template, wherein the data is processed by superimposition of the orthodontic aligner on the CT images of the patient including a jaw in axial and panoramic views. In this manner, the tooth above the gum line, represented by the negative impression as well as the tooth below the gum line, represented by the CT data is used to design the orthodontic aligner.
