A robotic system (9) for forming features in orthodontic aligners (18) includes a control system (8), a platen (13) for three-dimensional positioning of the aligner (18), a heating station (15) for selectively heating a small region of the aligner (18), and a thermoforming station (14) for manipulating the heated region to form a desired feature in the aligner (18). Optionally, a laser cutting and trimming station (16) can also be included to trim excess material from the aligner (18) or to cut features into the aligner (18). The control system (8) can include a processor with CAD software (11 ) to enable a user to design features for aligners (18).