A three-dimensional object printer comprises a platen, a gantry positioned above the platen, an ejector head positioned on the gantry, a sensor, and a controller. The controller is configured to operate the ejector to eject at least one drop of material toward the platen at an upper build level and determine process and cross-process differentials between a fiducial and the at least one drop of material deposited on the upper build surface. The controller is also configured to determine an ejector head shift in a process direction and a cross-process direction associated with each of the plurality of build levels based at least in part on the determined process and cross-process differentials and a number of build levels between the base build level and the upper build level.