The invention relates to planning orthodontic treatment for a patient, including surgery, using biological constrains such as those arising from bone, soft tissue, and roots of patient's teeth. The invention disclosed herein provides capability to vary the movement ratio between the teeth and bone and soft tissue through treatment simulation to assess the risk factor associated with a particular treatment plan. The invention further provides capability to monitor results of the treatment to determine the actual movement ratio between the teeth and bone and soft tissue and update the database. Additionally, a method and apparatus are disclosed enabling an orthodontist or a user to create an unified three dimensional virtual craniofacial and dentition model of actual, as-is static and functional anatomy of a patient, from data representing facial bone structure; upper jaw and lower jaw; facial soft tissue; teeth including crowns and roots; information of the position of the roots relative to each other; and relative to the facial bone structure of the patient; obtained by scanning as-is anatomy of craniofacial and dentition structures of the patient with a volume scanning device; and data representing three dimensional virtual models of the patient's upper and lower gingiva, obtained from scanning the patient's upper and lower gingiva either (a) with a volume scanning device, or (a) with a surface scanning device. Such craniofacial and dentition models of the patient can be used in optimally planning treatment of a patient.