This paper presents a system of 3-D micro structure measurement that uses an optical fiber probe of 5 µm in diameter. The probe is deflected when it comes into contact with a measured surface, and this deflection is measured optically. In this research, we optimize design parameters of optical system using ray tracing, and a prototype of the measuring system is fabricated on trial to verify the simulation results. Then, its measuring accuracies are examined by using the basic experimental apparatus. As a result, it is clarified that the resolution of the fiber probe is better than 10 nm. Also, the utility of this system is confirmed by measuring the shape of a 600 µm diameter ruby sphere.