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In plants in many industries, there exist a lot of transfer systems with vibration mechanisms. While transfer without residual vibration is usually demanded in these plants, this requirement necessitates large numbers of sensors and complicated models for control design. Therefore, This work presents a trajectory control design method to suppress residual vibration in transfer systems without the need to directly measure vibration. The proposed method consists of two parts. First, the frequency characteristics of the controller, comprised of control elements with simple structures such as a notch filter and a low-pass filter, are shaped as needed to suppress vibration. Next, various parameters of the control elements are determined by solving an optimization problem with penalty terms expressed by the constraints of both the time and frequency domains. The proposed method is applied to a liquid container transfer system, with special consideration given to the suppression of sloshing (liquid vibration) as well as to the maintenance of a high-speed transfer on the container's three-dimensional transfer path. The obtained controller demonstrates good performance for all demands. The effectiveness of the control design method is shown by experiments.