A method and apparatus are disclosed enabling an orthodontist or a user to create an integrated three dimensional digital model of dentition and surrounding anatomy of an orthodontic patient from a three-dimensional digital model obtained using a scanner with a three-dimensional digital model obtained using a Cone Beam Computed Tomography (CBCT) or Magnetic Resonance Tomography (MRT) imaging devices. The digital data obtained from scanning as well as from CBCT imaging are downloaded into a computer workstation, and registered together in order to create a comprehensive 3-D model of the patients teeth with roots, bones and soft tissues. The invention provides substantial improvement over the traditional two dimensional imaging modalities such as x-rays, photographs, cephalometric tracing for diagnosis and treatment planning.
