A computer implemented method for designing and/or manufacturing orthodontic appliances for use in treating or preventing temporomandibular joint dysfunction comprising: obtaining first bite scan data of a dentition of a patient with the patient's jaws in a target bite configuration; obtaining second bite scan data of the dentition of the patient with the patient's jaws in a natural bite configuration; and designing, based on said first and second bite scan data, a plurality of appliances configured to apply tooth-moving and jaw-moving forces to the patient's dentition so as to move the patient's dentition from the natural bite configuration to a final bite configuration corresponding to the target bite configuration through a sequence of incremental steps when the plurality of appliances is worn in succession, wherein each incremental step comprises tooth contact paths for a plurality of teeth of the patient's jaw; wherein: designing the plurality of appliances includes determining one or more gaps between upper teeth of the dentition and lower teeth of the dentition present during at least one of the incremental steps, adjusting positions of one or more occlusal surface features of at least one of said plurality of appliances to fill the one or more gaps to improve the tooth contact paths in at least one of the incremental steps when the appliance is worn by the patient, and optimizing the tooth contact paths for said incremental steps to avoid tooth collisions during said incremental steps, and one or more of the plurality of appliances is designed to apply tooth moving forces to modify said one or more gaps. obtaining first bite scan data of a dentition of a patient with the patient's jaws in a target bite configuration; obtaining second bite scan data of the dentition of the patient with the patient's jaws in a natural bite configuration; and designing, based on said first and second bite scan data, a plurality of appliances configured to apply tooth-moving and jaw-moving forces to the patient's dentition so as to move the patient's dentition from the natural bite configuration to a final bite configuration corresponding to the target bite configuration through a sequence of incremental steps when the plurality of appliances is worn in succession, wherein each incremental step comprises tooth contact paths for a plurality of teeth of the patient's jaw; wherein: designing the plurality of appliances includes determining one or more gaps between upper teeth of the dentition and lower teeth of the dentition present during at least one of the incremental steps, adjusting positions of one or more occlusal surface features of at least one of said plurality of appliances to fill the one or more gaps to improve the tooth contact paths in at least one of the incremental steps when the appliance is worn by the patient, and optimizing the tooth contact paths for said incremental steps to avoid tooth collisions during said incremental steps, and one or more of the plurality of appliances is designed to apply tooth moving forces to modify said one or more gaps. designing the plurality of appliances includes determining one or more gaps between upper teeth of the dentition and lower teeth of the dentition present during at least one of the incremental steps, adjusting positions of one or more occlusal surface features of at least one of said plurality of appliances to fill the one or more gaps to improve the tooth contact paths in at least one of the incremental steps when the appliance is worn by the patient, and optimizing the tooth contact paths for said incremental steps to avoid tooth collisions during said incremental steps, and one or more of the plurality of appliances is designed to apply tooth moving forces to modify said one or more gaps.