Recently to increase the productivity and improve the quality in the industrial process, suppressing the residual vibration in motion control systems becomes the essential problem to solve. One of the methods to suppress the residual vibration is the input shaping technique. It is based on parameters of the system model; however, the parameters are usually difficult to obtain. This paper shows the effects of the residual vibration caused by the variation of the general velocity profile for the system with two vibration modes, and also shows the effects of the input shaping filter based on the parameters of system model. Finally, the simulation results show that the proposed input shaping filter using an artificial immune algorithm is more effective for suppressing residual vibrations than genetic algorithm.