The tool axis misalignment, which causes machining inaccuracies in an active magnetic bearing(AMB)-spindle system, can be compensated by tracking control of the rotor-spindle. the pseudo-derivative feedback (PDF) control scheme alone does not correct the tool axis misalignment since the integral action results in the narrow bandwidth and large phase lag in the controlled system. To improve the tracking performance, the feedback and feedforward controllers are combined with the existing proportional-derivative controller, which stabilizes the inherently unstable AMB-spindle system dynamics. the theoretical and experimental results show that proposed control scheme efficiently compensates the tool axis misalignment compared with the conventional PDF control scheme.