The present invention is directed to computer-implemented methods of making a transfer tray using rapid prototyping techniques, where the gingival edge of the tray is defined to intersect with at least one receptacle for receiving an orthodontic appliance. This tray configuration helps to minimize the travel distance of the tray when placing the tray over a patient's teeth, while also preserving a high degree of mechanical retention for retaining the appliance until such time that the appliance is bonded to the tooth. Other aspects of the tray and associated methods of bonding are directed to a frangible web that extends over the gingival portion of the receptacle and fractures to facilitate tray removal after bonding.
