This paper describes multi-scale interface for bio and medical engineering based on MEMS technology. MEMS technology can provide various interfaces for biomedical application corresponding to hierarchical components of living organism such as cell, tissue, and organ. This paper mainly deals with small, soft, and safe (S3) micromachine as multi-scale interfaces for medical application. Micromachine is small in nature. S3 micromachine is based on its soft and flexible structure and safe driving principle. These features are suitable for advanced medical tools for minimally invasive medical operations. S3 micromachines-based medical tool has been applied to a retractor for spacing in front of the endoscope at our early stage. This paper also presents the S3 micromachine as a surgical tool for a cell sheet transplantation in an eye.