A method of operating a three-dimensional object printer, the method comprising: Operating at least one ejector of an ejector head to eject at least one first drop of material toward a first build surface provided on a platen at a first build level along a build axis; operating a sensor to measure first distance components of the first drop of material from a first fiducial reference on the first build surface, the first distance components including a first process direction component along a process axis and a first cross-process direction component along a cross-process axis; moving the ejector head relative to the platen along the build axis; placing a gauge block on the platen, the gauge block providing a second build surface at a second build level along the build axis; operating the at least one ejector of the ejector head to eject at least one second drop of material toward the second build surface; operating the sensor to measure second distance components of the second drop of material from a second fiducial reference on the second build surface, the second distance components including a second process direction component and a second cross-process direction component; calculating differentials between the first distance components and the second distance components, the calculated differentials including a process direction differential and a cross-process direction differential; determining an ejector head shift relative to the platen for a plurality of incremental build levels along the build axis between the first build level and the second build level, wherein the determined ejector head shift for each of the incremental build levels is based on the calculated differentials; and moving the ejector head and operating the at least one ejector to eject drops of material toward the platen in order to form a three-dimensional object, wherein moving the ejector head includes shifting the ejector head relative to the platen by the determined ejector head shift for each of the plurality of incremental build levels prior to ejecting drops of material at said incremental build levels. Operating at least one ejector of an ejector head to eject at least one first drop of material toward a first build surface provided on a platen at a first build level along a build axis; operating a sensor to measure first distance components of the first drop of material from a first fiducial reference on the first build surface, the first distance components including a first process direction component along a process axis and a first cross-process direction component along a cross-process axis; moving the ejector head relative to the platen along the build axis; placing a gauge block on the platen, the gauge block providing a second build surface at a second build level along the build axis; operating the at least one ejector of the ejector head to eject at least one second drop of material toward the second build surface; operating the sensor to measure second distance components of the second drop of material from a second fiducial reference on the second build surface, the second distance components including a second process direction component and a second cross-process direction component; calculating differentials between the first distance components and the second distance components, the calculated differentials including a process direction differential and a cross-process direction differential; determining an ejector head shift relative to the platen for a plurality of incremental build levels along the build axis between the first build level and the second build level, wherein the determined ejector head shift for each of the incremental build levels is based on the calculated differentials; and moving the ejector head and operating the at least one ejector to eject drops of material toward the platen in order to form a three-dimensional object, wherein moving the ejector head includes shifting the ejector head relative to the platen by the determined ejector head shift for each of the plurality of incremental build levels prior to ejecting drops of material at said incremental build levels.