In an aspect of the disclosure a three dimensional printing system includes an elevator mechanism for supporting a build plate, a printhead assembly, a movement mechanism, and a controller. The printhead assembly includes a printhead and a planarizer arranged along a scan axis. The movement mechanism is for scanning the printhead across the build plate. The controller is configured to: (a) print one or more base layers of ink onto the build plate, (b) print one or more layers of test patterns onto the base layers until an alignment determination can be made, wherein the test patterns comprise different timing values, and (c) receive information and update a scan axis timing parameter based on the determination.