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Linear motor direct-drive XY-table mechanisms commonly suffer from significant mechanical resonances at high acceleration rates. These problems can be solved by using a quantitative-feedback-theory-based tracking control scheme. This scheme has an inner-loop robust velocity controller, an outer-loop position controller and an auto-tuning feedforward compensator. A high order velocity controller is especially designed to reduce the resonance uncertainty as well as attenuating the external disturbances and sensor noises. The resulting control system is fully implemented and validated on a direct-drive XY-table with a maximum 6.8g (1g = 9.81 m/s2) high acceleration profile motion on tens of mass-production machines.