As the rapid progress in the development of optoelectronic components and computational power, 3D optical metrology becomes more and more popular in manufacturing and quality control due to its flexibility and high speed. However, most of the optical metrology methods are limited to external surfaces. This paper proposed a new approach to measure tiny internal 3D surfaces with a scanning fiber endoscope and axial-stereo vision algorithm. A dense, accurate point cloud of internally machined threads was generated to compare with its corresponding X-ray 3D data as ground truth, and the quantification was analyzed by Iterative Closest Points algorithm.