A system and method that is a web based application for creating and managing orthodontic laboratory prescriptions within a dental clinic or lab. The system receives a standard triangle language (STL) image file which has been obtained from an intraoral digital scan or cone-beam of a patient's mouth and teeth. The user manually selects brackets, attachments, bands, or other appliances and removes them from the 3D image file via a series of selections made through an interface within a digital workspace. The system then calculates a surface of the tooth that was disposed beneath the removed appliance and integrates it into the 3D image to create a clean 3D image of the patient's teeth free from any appliances. After the appliances have been removed, the user may further refine the image of the patient's teeth using a suite of tools including addition, deletion, smoothening, and definition tools.