Vibrational analysis is presented for a visual alignment system of nano-imprint process in this study. For a nano-imprinting equipment, the visual alignment system is one of the essential parts in order to align the mold into the target panel. For the precision alignment, the vibration from inside and outside of the vision system should be avoided, and the elimination of the vibration should be considered in the design process of the visual alignment design. In this work, vibrational characteristics for the vision system frame is analyzed and topology optimization of a frame section area is carried out. With the results of the analysis, a new frame design are suggested. Design consideration for constructing a visual alignment system in view of optimal design is also discussed.