In the flat panel display and semiconductor industries, the visual alignment system is considered as a core technology which determines the productivity of a manufacturing line. It consists of the vision system to extract the centroids of alignment marks and the stage control system to compensate the alignment error. In this paper, we develop a Kalman filter algorithm to estimate the alignment mark postures and propose a coarse-fine alignment control method which utilizes both original fine images and reduced coarse ones in the visual feedback. The error compensation trajectory for the distributed joint servos of the alignment stage is generated in terms of the inverse kinematic solution for the misalignment in task space. In constructing the estimation algorithm, the equation of motion for the alignment marks is given by using the forward kinematics of alignment stage. Secondly, the measurements for the alignment mark centroids are obtained from the reduced images by applying the geometric template matching. As a result, the proposed Kalman filter based coarse-fine alignment control method enables a considerable reduction of alignment time.