A method and apparatus for facilitating placement and evaluation of virtual appliances on virtual teeth of an orthodontic patient are described. Positioning references comprising bracket height, occlusal plane, or any arbitrary plane are provided to facilitate desired placement of virtual appliances on virtual teeth model. The process can be applied with any dentition state of a patient such as malocclusion, target state from treatment, or intermediate monitored state during the course of a treatment. An unified workstation for treatment planning provides the computer software tools for verification, simulation and evaluation of the virtual appliance placement. The process enables proper planning of treatment for an orthodontic patient suffering from malocclusion involving bonding of virtual brackets to the surface of the patient's virtual teeth with archwires placed in the slots of the brackets, so as to realize the desired results from the treatment in the most desired manner.