A method of making a transfer tray includes providing a physical mockup having a shape that corresponds to a positive shape of a patient's dental arch and a positive shape of one or more bracket analogs. A transfer tray may be formed over the physical mockup, with the transfer tray representing a negative replica of at least a portion of the mockup. One or more receptacles are accordingly formed in the ray, each receptacle approximating a least a portion of the shape of a bracket analog. A bracket associated with a bracket analog is placed into a receptacle of the one or more receptacles and a filler material is introduced into at least one receptacle.