Flexure mechanisms have been widely used for nanometer positioning systems. This article presents a novel conceptual design of an ultra-precision 3-degrees of freedom (XYθ(Z)) positioning system with nanometer precision. The main purpose of this novel stage design is for the application of measurement equipment, in particular biological specimens. The stage was designed as a hollow type and with a compact size for the inverted microscope. This stage includes piezoelectric transducer actuators, double compound amplification mechanisms, moving plate, and capacitor sensors. The double compound amplification mechanism was designed using a mathematical model and analyzed by the finite element method. Since the relationship between the variables of the hinge parameters and system performances are complicated, an optimization procedure was used to obtain the optimal design parameters, which maximized the system bandwidth. Based on the solution of the optimization problem, the design of the stage and FEM simulation results are presented. Finally, the stage was manufactured and tested.