A nano-imprinting stage has been widely used in various fields of nanotechnology. In this study, an analysis method of a nano-imprinting stage machine using FEM and flexible multi-body kinematics and dynamics has been presented. We have developed a virtual imprinting machine to evaluate the prototype design in the early design stage. The simulation using CAE for the imprinting machine is not only to analyze static and dynamic characteristics of the machine but also to determine design parameters of the components for the imprinting machine, such as dimensions and specifications of actuators and sensors. Structural components as the upper plate, the rotator, the shaft and the translator have been modeled with finite elements to analyze flexibility effects during the precision stage motion. In this paper flexible multi-body dynamic simulation is executed to support robust design of the precision stage mechanism. In addition, we made the 4-axis stage model to compare the dynamic behavior with that of 3-axis stage model.