Micro-milling requires both high speed and high accuracy in order to economically produce parts with features on the scale of 1 micron. Because micro-mills are small, they are more flexible than traditional large scale machines and therefore vibration is a problem. Since they also require high positioning precision, even small vibrations of the cutting tool are also an issue. This paper presents a nonlinear command shaping technique to reduce the vibrations of a micro-mill which can be implemented with a standard CNC controller. The robustness of this technique to modelling errors and disturbances is investigated. Theoretical proofs and experimental demonstrations of the command shaping technique are presented. The improved performance from the command shaping technique enables higher throughput and improved accuracy of the machine.