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Dual-drive gantry stages are used for high-speed high-precision motion control applications such as flat panel display manufacturing and inspection. Industrially, they are usually controlled using independent axis control without taking into consideration the effect of inter-axis mechanical coupling over positioning accuracy and precision. To improve this and minimize the effect of mechanical coupling over synchronization and tracking errors, we propose to model and control the dual-drive gantry stage on a decoupling basis. This approach allows representing the highly coupled Multiple Input Multiple Output (MIMO) system as a set of independent Single Input Single Output (SISO) systems. Based on this representation, a model-based feedback-feedforward control scheme is deduced. Experimental results show that the proposed decoupling basis control scheme leads to an improved motion control of the point-tool in comparison to the present industrial control.