This paper has described a system for measuring 3-D micro structures using an optical fiber probe. For this research, the stylus shaft with a diameter of 0.4 μm was fabricated using an acid-etch technique. Further, the minimum diameter of the available stylus shaft was examined using an FDTD method. Finally, the stylus characteristic and the measurement resolution were examined. As a result, it was shown by an FDTD simulation that the minimum diameter of the available stylus shaft was about 0.2 μm for a laser diode with a 375 nm wavelength. In addition, the stylus shaft with a diameter of 0.4 μm could be manufactured, and the resolution of the measurement system using this shaft was found to be approximately 5 nm.