A three dimensional printing system for fabricating a three dimensional article of manufacture comprising: an elevator mechanism for supporting a build plate; a printhead assembly configured to scan a printhead relative to the build plate along a scan axis, the printhead assembly including the printhead and a planarizer arranged along the scan axis whereby the planarizer leads or follows the printhead during a scan, the printhead including an ejector face, the planarizer defining a planarizing plane that is offset downwardly from the ejector face by a trajectory height H T; a movement mechanism for scanning the printhead assembly relative to the build plate; and a controller configured to: (a) operate the printhead and the movement mechanism to eject one or more base layers of ink onto the build plate while maintaining the build plate at a fixed vertical height until a cumulative thickness of the base layers of ink reach at least a base height H B at which the planarizer begins to engage the layers of ink or is proximate to an upper surface of the base layers; (b) repeatedly print a layer of a test pattern onto the base layers and increment the base downwardly by a layer thickness for a plurality of test pattern layers until an alignment determination can be made, wherein the test patterns comprise different timing values, and wherein a timing value is a start time for a nozzle to begin ejecting drops to form a pattern segment of the test pattern; (c) receive information based upon the test patterns; and (d) update system timing parameters to more accurately align the three dimensional printing system along the scan axis. an elevator mechanism for supporting a build plate; a printhead assembly configured to scan a printhead relative to the build plate along a scan axis, the printhead assembly including the printhead and a planarizer arranged along the scan axis whereby the planarizer leads or follows the printhead during a scan, the printhead including an ejector face, the planarizer defining a planarizing plane that is offset downwardly from the ejector face by a trajectory height H T; a movement mechanism for scanning the printhead assembly relative to the build plate; and a controller configured to: (a) operate the printhead and the movement mechanism to eject one or more base layers of ink onto the build plate while maintaining the build plate at a fixed vertical height until a cumulative thickness of the base layers of ink reach at least a base height H B at which the planarizer begins to engage the layers of ink or is proximate to an upper surface of the base layers; (b) repeatedly print a layer of a test pattern onto the base layers and increment the base downwardly by a layer thickness for a plurality of test pattern layers until an alignment determination can be made, wherein the test patterns comprise different timing values, and wherein a timing value is a start time for a nozzle to begin ejecting drops to form a pattern segment of the test pattern; (c) receive information based upon the test patterns; and (d) update system timing parameters to more accurately align the three dimensional printing system along the scan axis. (a) operate the printhead and the movement mechanism to eject one or more base layers of ink onto the build plate while maintaining the build plate at a fixed vertical height until a cumulative thickness of the base layers of ink reach at least a base height H B at which the planarizer begins to engage the layers of ink or is proximate to an upper surface of the base layers; (b) repeatedly print a layer of a test pattern onto the base layers and increment the base downwardly by a layer thickness for a plurality of test pattern layers until an alignment determination can be made, wherein the test patterns comprise different timing values, and wherein a timing value is a start time for a nozzle to begin ejecting drops to form a pattern segment of the test pattern; (c) receive information based upon the test patterns; and (d) update system timing parameters to more accurately align the three dimensional printing system along the scan axis.