A method, comprising positioning a plurality of digital bite adjustment structures at locations on a corresponding plurality of digital tooth receiving cavities of a digital model of an appliance for a first jaw at a first stage of a treatment plan； designing the bite adjustment structures to have a first shape and location specific to the first stage of a treatment plan designed to interface with teeth of a second jaw； adjusting the bite adjustment structures by changing the position of the plurality of digital bite adjustment structures on the corresponding plurality of digital tooth receiving cavities of the digital model of the appliance of the first jaw at a second stage of the treatment plan； and outputting the digital model of the appliance of the first jaw for fabrication of physical models corresponding to the appliance of the first jaw at the first and the second stages of the treatment plan for formation of physical appliances.
