The purpose of this study is to design a disturbance observer for a micro-stepping stage to eliminate the disturbances from cables, friction, mass unbalance of the moving part, etc. The disturbance observer is designed for air-floating X-Y precision micro-stepping X-Y stage which widely used in stepper machine or semiconductor manufacturing systems. The micro-stepping X-Y stage has a weak point of the variation of characteristics with position locations, which caused by various disturbances. In this study, it will be described that a simple and high throughput disturbance observer algorithm improves the dynamic error and settling time of the micro-stepping stage.