It is necessary to design the anti-vibration system of precision machinery for a quality assurance. However, in general, the allowable vibration limit is not well known. In this paper, the vibration criteria for foundation of sensitive machinery is proposed and anti-vibration system is designed by using vibration measurement results of foundation. Also, the finite element analysis is performed to verify the effectiveness of the designed anti-vibration system and to determine the allowable dynamic loads of precision measuring system. The results of this study will be helpful for the future design of anti-vibration structures with nano scale measuring system.