In modern manufacturing industries, many applications require precision motion control of multi-agent systems, like multi-joint robot arms and multi-axis machine tools. Cutter (end effector) should stay as close as possible to the reference trajectory to ensure the quality of the final products. In conventional computer numerical control (CNC), the control unit of each axis is independently designed to achieve the best individual tracking performance. However, this becomes less effective when dealing with multi-axis contour following tasks because of the lack of coordination among axes. This dissertation studies the control of multi-axis machine tools with focus on reducing the contour error. The proposed research explicitly addresses the minimization of contour error and treats the multi-axis machine tool as a multi-input-multi-output (MIMO) system instead of several decoupled single-input-single-output (SISO) systems. New control schemes are developed to achieve superior contour following performance even in the presence of disturbances. This study also extends the applications of the proposed control system from plane contours to regular contours in R3. The effectiveness of the developed control systems is experimentally verified on a micro milling machine.