As the size of LCD panel grows larger, the importance of the accurate assembly of glasses increases. Various Run-to-Run controllers are used to arrange the locations of transistors and color filter printed on each glass. When the contour of a panel on the glass is distorted than others, however, overall differences of each panel are increased in order to diminish the relatively large discrepancy in the distorted panel; this situation causes many defective panels. In this paper, some optimization models will be presented to resolve this problem. By setting the tolerance limit of the acceptable panel as a constraint, an optimization problem, which maximizes the acceptable panels, is solved to find the optimal recipe of panel assembly process. Numerical experiments are conducted to show its efficiency.