Abstract: A system and method that is a web based application for creating and managing 3D models used in orthodontic laboratory prescriptions within a dental clinic or lab. The method includes automatically detecting and removing any appliances contained within the 3D image file. After the appliances have been removed, the system then automatically replaces the removed image data with new image data that is calculated to approximate the surface of the tooth disposed beneath the deleted appliance in order to create a clean, second 3D image. The method may further automatically refine the second 3D image of the patients teeth or delete any artifacts which remain after creation of the second 3D image. The second 3D image may then be used as the basis on which to change the patients orthodontic or dental prescription.