A method and system for orthodontic treatment planning, evaluation and quality measurement is provided comprising a workstation having computing platform, a graphical user interface, a processor and a computer storage medium containing digitized records pertaining to a patient. The digitized records include image and other types of data. The computer storage medium further includes a set of software instructions providing graphical user interface tools for providing a user with access to the digitized records for planning orthodontic treatment of a patient. Also provided are reference databases for aiding in the decision process during treatment selection, treatment planning and treatment delivery and progress monitoring and evaluation. Also provided are parameter or criteria measurement techniques and generally acceptable thresholds, which can be updated through learning process and through acquisition of patient data. Once the treatment is planned, the virtual dentition model of the patient in the proposed treatment set-up or the target state is evaluated using several virtual model evaluation features and criteria.