With the increasing demand for VBNS and VDSL, the development of the kernel parts of optical communication such as PLC(Planar Light Circuit), Coupler, and WDM elements has increased. The optical transmitter and the receiver module need precise and mechanical alignment within a few micrometers to couple the semiconductor device, optical fiber and waveguide. The alignment and the attachment technology are very important in the fabrication of an optical element. Presently, the alignment of the optical element is time consuming, and an effective alignment algorithm has not yet to be developed. In this paper, the optical element alignment of the multi-axis ultra precision stage is studied. Two alignment algorithms applied to the ultra precision multi-axis stage are used, the field search algorithm and the peak search algorithm. The automation program to improve the characteristics of the optical element alignment system is developed by Labview programming and is composed of three tabs, the field search tab, plotting tab and peak search tab. The developed program is applied to an actual system to determine the improvement in alignment performance.