A stage positioning system and method for aligning optical components according to a figure of merit is disclosed. The system includes a stage assembly having six axes of freedom wherein the pivot point of the stage assembly motion is user definable and preferably outside the envelope formed by the stage assembly. The stage assembly includes three sub-assemblies. A base sub-assembly provides x and z axes motion, a yaw stage provides yaw about the y axis, and a three-axis stage provides y motion as well as pitch and roll about the x and z axes, respectively.