A method of making transfer apparatus for use in indirect bonding of orthodontic appliances includes the act of applying a spacer material over a dentition replica. The spacer material includes at least one cavity for releasably receiving an orthodontic appliance, and a base of the appliance is in contact with one of the teeth of the dentition replica. A tray is formed over the spacer material and the spacer material is then removed. Subsequently, a quantity of matrix material is directed into the space between the tray and the dentition replica in order to releasably hold the appliance for an indirect bonding procedure.