An $XY{ heta}$ stage for large area UV Nano-Imprinting Lithography (UV-NIL), which consists of linear actuators, translational/revolute joints, etc., has been modeled as flexible bodies. Multi-layer alignment control for the translation and angle offset cancellation has been performed in a virtual simulation environment using both ADAMS/Control and Matlab/SIMULINK. Furthermore, the vertical motions of three and four axis stages during the control action have been analyzed and compared to each other. The performed analysis can provide useful information for a high precision NIL stage development in the future.