The kinematics and control problem of a visual alignment system is investigated, which plays a crucial role in the fabrication process of flat panel displays. The first solution is the inverse kinematics of a 4PPR parallel alignment mechanism. It determines the driving distance of each joint to compensate the misalignment between mask and panel. Second, an efficient vision algorithm for fast alignment mark recognition is suggested, where by extracting essential feature points to represent the geometry of a mark, the geometric template matching enables much faster object recognition comparing with the general template matching. Finally, the overall visual alignment process including the kinematic solution, vision algorithm, and joint control is implemented and experimental results are given.