National Research Institute for Earth Science and Disaster Prevention (NIED) is constructing a three-dimensional large-scale shaking table. For developing useful methods of operation and control for the table, we have started the study of operation and control for a small-scale shaking table, and then continued the study for a medium-scale shaking table. A final goal of the study is to obtain a guideline of operation and control for the large-scale shaking table. In this paper, the authors treat the study of operation and control for the medium-scale shaking table. The characteristics of the medium-scale shaking table with a non-linear structure are experimentally identified with displacement feedback control (Conventional Control). Control experiments were performed with the Conventional and the Minimal Control Synthesis (MCS) procedures. The MCS procedure has been proved to be effective to enhance the performance of the control for the medium-scale shaking table with a non-linear structure.