A method for manipulating a three-dimensional model of a patient's teeth for making one or more tooth positioning appliances involves: forming at least one three-dimensional model of the patient's teeth; acquiring an initial digital data set representing at least part of the three-dimensional model; manipulating a digital model derived from the initial digital data set to move at least one tooth from an initial position to a first intermediate position; forming a first guide from the digital model with the at least one tooth in the first intermediate position; separating the at least one tooth from the three-dimensional model; placing the at least one tooth in the first guide in the first intermediate position; and securing the at least one tooth to the three-dimensional model in the first intermediate position. Guide apparatus and systems are also provided.