A system and associated methodology for the generation of digital models that account for the adaptation of the shape of the patient's gingiva is provided. The exemplary system uses an initial scan of the patient's gingiva as a base model, taking into account the type and morphology of the teeth, the shape, orientation and movements of the roots inside the gingiva, and other factors for a more accurate prediction of the changes in the shape of the gingiva throughout every step of the treatment. In particular, the system proactively determines the areas of the model that will be covered by the aligner and prevents changes to such areas, whereas the shape of the model outside these areas is altered in a way to minimize the size of model and to add any necessary features for the manufacturing of the aligners.
