A system to manufacture orthodontic appliances, program product, and associated methods are provided. An embodiment of a system can include a virtual orthodontic appliance design computer having orthodontic appliance design program product provided to design a virtual dimensional representation of an orthodontic appliance including bracket bodies and bracket pads, and a mold apparatus positioned to form each bracket body and bracket pad. The system also includes a data processing computer including computer-aided manufacturing program product provided to derive electrical discharge device control instructions including a virtual dimensional representation of a bracket slot in the bracket, and an electrical discharge machining apparatus. The electrical discharge machining apparatus can include a controller including control program product to derive a control signal carrying the electrical discharge device control instructions and an electrical discharge device.