A quantity of a photocurable composition, such as an orthodontic adhesive containing a photoinitiator, is placed between the base of an orthodontic appliance and a replica of a patient's tooth structure. The replica is made using a material that transmits actinic radiation. As the appliance is pressed into firm contact with the replica tooth structure, an outer surface of the photocurable composition assumes the configuration of the underlying portion of the replica tooth structure. Actinic radiation is then directed to the photocurable composition, and at least part of the actinic radiation is directed through the replica tooth model in order to harden the photocurable composition. The hardened composition provides a contoured bonding surface having a shape that matches corresponding regions of the patient's tooth structure. Methods are also disclosed for making an orthodontic indirect bonding transfer apparatus for use with appliances having a contoured bonding surface.