An indirect bonding apparatus is made by initially placing spacer material over a replica of the patient's tooth structure. A tray is then formed over the spacer material and hardened. Next, the spacer material is removed from the tooth replica and orthodontic appliances are placed on the replica at desired locations. A matrix material is placed between the tray and the replica and allowed to harden. Optionally, the apparatus includes features for facilitating removal of the transfer apparatus after the bonding procedure has been completed, and features for applying firm, uniform pressure to the appliances during the bonding procedure. Other aspects of indirect bonding are also described.