Abstract: The present invention is a method for performing a calibration routine of a deposition device in a three-dimensional modeling machine that deposits a material to build up three-dimensional objects as directed by a controller on a substrate mounted on a platform. The method comprises generating a material build profile, which represents a three-dimensional structure at defined locations. A relative position of the material build profile is then determined. An expected build profile is identified and then compared to the determined relative position of the material build profile to identify any difference which represents an offset. The modeling system then positions the deposition device based upon the offset.