A method of indirect bonding and a physical model that allows for optimal positional alignment of orthodontic appliances on a patient's teeth is disclosed. The physical model of the patient's teeth has pods and ridges on the facial surface of the teeth. Adhesive is applied to an orthodontic appliance and the appliance is placed on a tooth of the physical model against the ridge and on top of the pods. The adhesive fills the space in between the appliance and the facial surface of the tooth and adheres to the model, resulting in a dimensionally correct custom base that is properly aligned with the tooth to account for all five positional elements of a tooth. Once all the orthodontic appliances are applied to the model, the appliances can then be removed from the model and bonded to the patient's teeth in the optimal position using a transfer template.