Described herein are systems and methods for marking models for dental aligner fabrication. A method for producing a physical model of teeth including a three-dimensional marking includes receiving a first digital model of teeth in an alignment position and selecting a location for marking a physical model of the teeth in the alignment position with a three-dimensional marking, the physical model to be fabricated based on the first digital model. The method also includes generating a second digital model of the teeth in the alignment position based on the first digital model, the second digital model representing the physical model and including the three-dimensional marking at the marking location, and using a three-dimensional fabrication method to fabricate the physical model including the three-dimensional marking from the second digital model.
