Precise positioning stages are often employed for precise machinery. For the purpose of vibration isolation, these precise positioning stages are mounted on a heavy base structure which is supported by compliant springs. Then the base structure is subjected to residual vibration due to the reactive force and vertical moving load induced by the stage motion. This paper investigates the vibration behavior of a positioning stage base and the associated vibration suppression technique. A dynamic model is developed to investigate the base vibration due to the reactive force and moving load effects by the moving stage. An input shaping technique is also developed to suppress the residual vibrations in base structures. Simulations and experiments show that the developed dynamic model adequately represents the base vibration and that the proposed input shaping technique effectively removes the residual vibrations from the positioning stage base.