The orthodontic alignment of misaligned teeth includes preparing a digital and/or physical overlay model which is the superimposed positioning of the patient's original misaligned dentition with the target or final position. The superimposition of one upon the other creates an open space through which teeth may move in a natural manner, allowing for a treatment plan that takes into account the physical interaction of one tooth with another or the differences in tooth movement rates due in part to differences in underlying bone density or the like. An aligner tray fabricated using the model will likewise represent the before and after tooth positions and will also have the open space to allow tooth movement. Force exerting structures are preferably placed into the aligner tray to impinge upon the patient's teeth in a prescribed manner when the aligner tray is inserted into the patient's oral cavity.