An alignment system for optical lithography uses cameras fixed to a movable stage and to a lithography unit to view unique microscopic non-uniformities that are inherent to the surface of a work piece, e.g., metal or ceramic microcrystalline grains, for position referencing. Stage cameras image two sites on the work piece through windows in the stage to establish original position templates. After the work piece has been repositioned, e.g., reversed topside-down, the same two sites are again viewed and template matching establishes the transformed coordinates of the work piece, e.g. by a lithography unit camera under which the stage moves to approximate site locations. Two corner cameras can serve as a coarse positioning mechanism. The alignment system is particular useful for backside alignment in printed circuit board lithography.