A method and system are disclosed for quickly arriving at a pre-set-up for the orthodontic treatment of a patient based up on the user specified parameters; and thereafter enabling the user in interactively arriving at a final, desired treatment set-up for the patient. Several sub-operations are disclosed for arriving at the orthodontic pre-set-up. These sub-operations can be arranged in a specific sequence for realizing the orthodontic treatment pre-set-up for a patient. According to another aspect of the invention, a global reference system is disclosed that enables consistent treatment planning. The global reference system prevents unintended tooth displacements caused as side effects to the desired tooth displacements.