Herein are provided methods, systems, computer-readable media, techniques and processes for surface manipulation in dental prosthesis design. These include providing an interface for modifying the surface of a model of a dental prosthesis. This interface may be provided to an operator, dentist, dental practitioner, or any other appropriate person via a computer and a computer display. The operator provides areas in which the operator would like to add a layer or other limited manipulation to the surface of the model. This may include an addition to the surface or a subtraction from the surface. As the operator is defining additional areas to manipulate on the surface (e.g., add or subtract a layer), invariably some of them will overlap. Unlike previous methods, this overlap will not cause the amount added to the surface to increase beyond the predefined limit for the layer. This allows operators to define cleanly added layers or cleanly subtracted layers from dental prostheses.