A method and alignment system for minimizing errors in the deposition of films of tailored thickness. A first position on a stage is identified for optimal placement of a downward looking microscope (DLM) and an upward looking microscope (ULM) when alignment marks on the DLM and ULM are aligned, where the DLM is attached to a bridge and the ULM is attached to the stage. A second position on the stage is identified when the ULM on the stage is aligned with the alignment marks on a metrology tool. A surface of a chucked substrate affixed to the stage is then measured. A map between a substrate coordinate system and a metrology coordinate system may then be obtained using the measured surface of the chucked substrate with the first and second positions.