Generally, the integrated system using ion beam consists of 4 major parts, which are SEM, FIB, nano stage, and chamber. Among them, the nano stage and the chamber are designed and manufactured. The whole systems are integrated. Also, FE models are built to perform modal analyses of each part and the whole integrated system with a commercial program. Through these analyses, it is found that each part and the integrated system are very safe against vibrations including external excitations from ground and any others, because their natural frequencies are much larger than frequencies of external excitations. Also, isolation of ground induced vibration is considered.