For synchronization of high-precision stage systems, in particular the synchronization between a wafer and a reticle stage system of a wafer scanner, a master–slave controller design is presented. The design consists of a synchronization controller based on FIR filters and a data-driven self-tuning approach is used to find the coefficients of these filters. In the context of Lur'e systems, i.e. the reticle stage slave system has a variable gain controller with saturation nonlinearity, a part of the gradients needed for self-tuning is obtained from reconstruction using closed-loop nonlinear models. The remaining part is given by sampled data obtained primarily from time-series measurements. Performance with the synchronization controller is ...