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This work presents a real-time time-delay filtering approach for reference shaping of high precision motion control of vibratory systems. The motion of the system is initiated with a judicious (arbitrary) step command and the acquired motion data is used to estimate the modal parameters in realtime.The modal data is subsequently used to synthesize the subsequent step commands to mitigate the residual vibrations. The proposed control algorithm is tested on a gantry crane structure with a suspended payload. Our method estimates the system parameters based on computer vision while tracking an ArUco fiducial marker which is integral with the payload. Computational efficiency is ensured by using C++ to deploy the algorithm. The goal is to minimize the residual energy at the terminal displacement for rest-to-rest maneuvers of a suspended payload with unknown dynamics. An inertial measurement unit is used to track the pendular angular velocity at the end of the maneuver and is not used in the model identification process.