Iterative learning control (ILC) is a known technique for improving the performance of systems or processes that operate repetitively over a fixed time interval. ILC generates a feed-forward signal effective for providing good tracking control. Experience with ILC algorithm applied to the wafer stage of a wafer scanner motion system has shown that ILC has liability to deal with limited performance in the face of position dependent dynamics, with the fact that ILC does not account for setpoint trajectory changes and with stochastic effects. The goal of the research presented in this paper is to integrate ILC applied to the wafer stage motion system with time-frequency analysis. This provides insight into the above mentioned ILC shortcomings when the learning control technique is applied on the considered motion system. We examine the suitability of a time-frequency adaptive filtering design for the learned feed-forward when applied to the wafer stage setup.