An improved multi-axis gas bearing stage assembly is disclosed which has a base (16), an intermediate stage element (24), a stage (11), and a control system for controlling the movement of the intermediate stage element and the stage. The control system includes first and second Y-axes positioning sub-systems for differentially positioning first and second ends of the intermediate stage element (24) along first and second Y-axes of motion, with respect to the base. and an X.-axis positioning sub-system (98) for positioning the stage along an X i -axis of motion, with respect to the intermediate stage element (24). The positioning sub-systems comprise linear motors (84,86,98), measuring scales (102,104, 106), and read heads (108,110,112). A method of achieving orthogonality between the Y- and X i -axes that features on orthogonality alignment standard is as well disclosed.