This paper deals with precise positioning of a high-speed positioning stage without inducing residual vibration by using an input shaping technique. Input shaping is well known to be a very effective tool for suppressing the residual vibration of flexible structures. However, the ordinary input shaping for positioning stages is designated mostly for velocity regulation, not for the residual vibration at the target position. The main difficulties in implementing input shaping along with precise positioning are the time delay caused by the servo system characteristics and the s-curve feature often employed in some motor controllers. This paper analyzes the dynamic responses of a single-mode-dominate stage system subjected to input shaping. A theoretical model is developed io investigate the nature of system. In order to overcome the difficulty, this paper proposes an improved input shaper based on modified command profile generation. The proposed method is proved effective through experiments and simulations.