Methods for generating intermediate stages for orthodontic aligners using machine learning or deep learning techniques. The method receives a malocclusion of teeth and a planned setup position of the teeth. The malocclusion can be represented by translations and rotations, or by digital 3D models. The method generates intermediate stages for aligners, between the malocclusion and the planned setup position, using one or more deep learning methods. The intermediate stages can be used to generate setups that are output in a format, such as digital 3D models, suitable for use in manufacturing the corresponding aligners.