An integrated system is described in which digital image data of a patient, obtained from a variety of image sources, including CT scanner, X-Ray, 2D or 3D scanners and color photographs, are combined into a common coordinate system to create a virtual three-dimensional patient model. Software tools are provided for manipulating the virtual patient model to simulation changes in position or orientation of craniofacial structures (e.g., jaw or teeth) and simulate their affect on the appearance of the patient. The simulation (which may be pure simulations or may be so-called "morphing" type simulations) enables a comprehensive approach to planning treatment for the patient. In one embodiment, the treatment may encompass orthodontic treatment. Similarly, surgical treatment plans can be created. Data is extracted from the virtual patient model or simulations thereof for purposes of manufacture of customized therapeutic devices for any component of the craniofacial structures, e.g., orthodontic appliances.