A stage assembly (8) includes a first stage (10) having at least one degree of freedom, i.e. at least one long stroke motion capability, and being movably mounted in a first stage base frame (12), the first stage base frame permitting motion in a first direction. A second stage (20) has at least one degree of freedom, i.e. at least one long stroke motion capability, and being movably mounted in a second stage base frame (22). The second stage base frame permitting motion in a second direction which is different from the first direction. The first stage and the second stage are located one over the other in a third direction which is orthogonal the first and second directions and a motion. An isolated reference metrology frame (18) is configured to provide a point of reference for the first and second stages in one or more degrees of freedom. Other degrees of freedom may be measured more directly from one stage relative to the other.