Increasingly stringent performance requirements for motion control necessitate the use of increasingly detailed models of the system behavior. Motion systems inherently move, therefore, spatio-temporal models of the flexible dynamics are essential. In this paper, a two-step approach for the identification of the spatio-temporal behavior of mechanical systems is developed and applied to a lightweight prototype industrial wafer stage. The proposed approach exploits a modal modeling framework and combines recently developed powerful linear time invariant (LTI) identification tools with a spline-based mode-shape interpolation approach to estimate the spatial system behavior. The experimental results for the wafer stage application confirm the suitability of the proposed approach for the identification of complex position-dependent mechanical systems, and its potential for motion control performance improvements.