Optical fibers are indispensable fer optical communication systems that transmit large volumes of data at high speed. But the aligning technology under the sub-micron accuracy is required for the precise axis adjustment and connection. For the purpose of precise alignment of the optical arrays, in this research, we have developed the 12-axis(with 8 automated axis and 4 manual axis) automatic optical fiber alignment system including the image processing-based searching system, the automatic loading system using the robot and the suction toot and the automatic UV bonding system. In order to obtain the sub-micron alignment accuracy, two 4-axis PC-based motion controllers and the two 50nm resolution 6-aixs micro-stage actuated by micro stepping motors are adopted. The fiber aligning procedure consists of two steps. Firstly, the optical wave guide and an input optical array are aligned by the 6-axis input micro-stage with the IR camera. The image processing technique is introduced to reduce primary manual aligning time and result in achieving the 50% decrease of aligning time. Secondly, the IR camera is replaced by the output micro-stage and a wave guide and two optical arrays are aligned simultaneously before the laser power intensity delivered to the optical powermeter reached the threshold value. When the aligning procedure is finished, the wave guide and arrays are W bonded. The automatic loading/unloading system is also introduced and the entire wave guide handing time is reduced significantly compared to the former commercial aligning system.