Nowadays, the researches for improving LCD manufacturing process and reducing cost are getting accelerated and additionally new types of process are widely developed. In this situation, APEM(Anti Photo Exposure Method) which does not need photo-lithography is realized as one of possible alternative of LCD process. APEM makes LCD pattern by stamping and it can reduce the process cost and process time because of its simplicity. But optical alignment between pattern glass and target glass is very critical fact to realize the precise patterns. So, the analysis of deflection of large size of glass is carried out and design of experiment method is applied for optimal design of jig.