A method of making a transfer tray for bonding an orthodontic appliance comprising: obtaining a virtual model of a patient's dental structure; determining a desired location for a virtual orthodontic appliance on the model; providing a virtual receptacle sufficient to releasably retain the appliance at the desired location, wherein the virtual receptacle has a configuration that matches at least a portion of the appliance; deriving a virtual tray body extending across at least a portion of the model and at least a portion of the receptacle remote from the model, wherein the act of deriving a virtual tray body includes the act of defining a gingival edge of the tray body that intersects the virtual receptacle; rendering a virtual stop member that connects to the tray body and matches at least a portion of the virtual model, wherein the virtual stop member includes a posterior section (27,29) that matches a portion of a molar tooth and an anterior section that matches a portion of an anterior tooth, wherein the virtual stop member further includes a flexible section that connects the posterior section (27,29) and anterior section to each other, and wherein the flexible section has a generally rectangular cross-section in a plane normal to its longitudinal axis and wherein the cross-section has an occlusal-gingival dimension greater than its facial-lingual dimension; and forming the transfer tray by rapid prototyping, wherein the transfer tray includes a physical tray body and a physical receptacle that correspond to the virtual tray body and virtual receptacle respectively, wherein the transfer tray further includes a physical stop member that corresponds to the virtual stop member and wherein the physical tray body has a first Shore hardness and the physical stop member has a second Shore hardness that is greater than the first Shore hardness. obtaining a virtual model of a patient's dental structure; determining a desired location for a virtual orthodontic appliance on the model; providing a virtual receptacle sufficient to releasably retain the appliance at the desired location, wherein the virtual receptacle has a configuration that matches at least a portion of the appliance; deriving a virtual tray body extending across at least a portion of the model and at least a portion of the receptacle remote from the model, wherein the act of deriving a virtual tray body includes the act of defining a gingival edge of the tray body that intersects the virtual receptacle; rendering a virtual stop member that connects to the tray body and matches at least a portion of the virtual model, wherein the virtual stop member includes a posterior section (27,29) that matches a portion of a molar tooth and an anterior section that matches a portion of an anterior tooth, wherein the virtual stop member further includes a flexible section that connects the posterior section (27,29) and anterior section to each other, and wherein the flexible section has a generally rectangular cross-section in a plane normal to its longitudinal axis and wherein the cross-section has an occlusal-gingival dimension greater than its facial-lingual dimension; and forming the transfer tray by rapid prototyping, wherein the transfer tray includes a physical tray body and a physical receptacle that correspond to the virtual tray body and virtual receptacle respectively, wherein the transfer tray further includes a physical stop member that corresponds to the virtual stop member and wherein the physical tray body has a first Shore hardness and the physical stop member has a second Shore hardness that is greater than the first Shore hardness.