In a multiple degrees of freedom motion system with rigid-flexible coupling, the flexible internal dynamics have a significant negative impact on performance because the degrees of freedom are coupled. Inspired by this problem, a multi-input multioutput state-space model based on modal coordinates is proposed to decouple the rigid body and flexible modes. The closed-loop subspace identification method based on orthogonal is utilized to develop an unbiased standard state-space model. Based on the similarity principle, a modal analysis method is proposed to transfer the standard state-space model to the proposed modal-decomposition-dependent state-space model. Controllability and observability criteria are met to guarantee the minimum realization of the proposed state-space model. Finally, a modeling and modal analysis experiment is conducted on a developed wafer stage of lithographic tool. The results verify the effectiveness and accuracy of the proposed modeling method, as well as the controllability and observability of the proposed model.