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It is well known that microstepping reduces the resonance behavior of stepping motors since the rotor moves in a sequence of very small steps. However, the under-damped nature of the motor does not change. In this paper, a scheme that uses microstepping and closed loop position control to stabilize and reduce resonance damping of the motor is proposed. The motor currents are controlled in a frame rotating synchronously with the excitation frequency. The d-axis current provides the torque to oppose the external load, and the q-axis current provides the transient torque to damp the motor. The motor velocity and position are estimated via an observer that tracks the angle of the motor back EMF voltage. The response of the closed loop system is independent of the external load level. Both simulation and experimental results have shown that the proposed control scheme is very effective in damping out the resonance of microstepping-controlled motors.