A nano-stage simulation tool is developed for an advanced E-beam lithography system. Even if piezo-actuators are believed to be compatible fer the E-beam lithograpy system it is difficult to predict their characteristics due to their nonlinearities such as hysteresis and creep. In this paper, the nonlinear properties are modeled for a piezo-actuator by considering the voltage range and speed variations. The hysteresis is described as the first order differential equation with 24 sets of parameters and the creep is modeled as a time-dependent logarithmic function with 2 sets of a parameter. A two-axis nano stage with piezo-actuators are investigated for realizing nano scale motions. The characteristics of flexure guide mechanisms are analyzed based on the finite element method using the ANSYS software. The simulation tool for the nano stage is constructed by using the RecurDyn software. The dynamic response of the nano stage is obtained in simulations and compared with the experimental data.