Precision stages for 6-DOF positioning, actuated by PZT stacks, which are fed back by gap sensors and guided by flexure hinges, have enlarged their application territory in micro/nano manufacturing and measurement area. The precision stages inherently have such limitations as the nonlinearity between input and output in piezoelectric stacks, feedback signal noise in precision capacitive gap sensors and low material damping in precision kinematic linkages of mechanical flexures. To surmount these limitations, the precision stage is modeled with physics-based variables, which are identified by transient response correspondence, and a gain margin calculation algorithm using the Prandtl-Ishlinskii model and describing function is newly developed to assess system performance more precisely than linear controller design schemes. Based on such analyses, a precision positioning controller is designed. Excellent positioning accuracy with rapid settlement accomplished by the controller is shown in step responses of the closed-loop system.