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Widely used for high-speed high-precision motion control in the electronics, nuclear and automotive industries, gantry stages are usually controlled using independent axis control. In order to avoid the effects of the mechanical coupling over synchronization and tracking errors, we propose a control on a modal reference frame. First, the system is modeled with respect to the center of mass of the moving beam and a modal transformation is applied to obtain the motion equations on a decoupling base. Next, a model-based control scheme is deduced with the minimization of synchronization and tracking errors as objectives. Finally, experimental results show that the proposed modal control scheme leads to an improved motion control of the point-tool in comparison with the present industrial control.