Indirect bonding trays for orthodontic treatment are made from a model of the patient's dental arch that is manufactured using digital data and rapid prototyping processes. The model includes one or more guides for orienting an orthodontic appliance in a desired position on a model tooth of the dental arch model. A holder is connected to the archwire slot of the appliance and is brought into contact with the guide in order to move the appliance to its intended position for subsequent manufacture of the indirect bonding tray.