A 4-DOF manipulator is developed to carry mask-plates of integrated-circuit lithography. Its three translation axes are driven with servo motors, and its rotation axis is driven with a step motor. The manipulator is controlled with a programmable controller to execute two movement categories. One is the transport in large range, which is a feedback system with two loops such as position loop and velocity loop. Another is the alignment in small range, which is a feedback system with three loops including aligning loop, position loop, and velocity loop. The aligning errors are measured with two four-quadrant photodetectors. The property of the detectors is investigated, and a novel control strategy for alignment is proposed. Experiments were well conducted to verify the effectiveness of the proposed control system and algorithms.