This paper presents a system that can be used for micro-hole measurement; the system comprises an optical fiber stylus that is 5 µm in diameter. The stylus deflects when it comes into contact with the measured surface; this deflection is measured optically. In this study, the design parameters of the optical system are determined using a ray-tracing method, and a prototype of the probing system is fabricated to verify ray-tracing simulation results; furthermore, the performance of the system is evaluated experimentally. The results show that the design parameters of this system can be determined using ray-tracing; the resolution of the measurement system using this shaft was approximately 3 nm, and the practicality of this system was confirmed by measuring the shape of a micro-hole 100 µm in diameter and 475 µm in depth.