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The nanoindentation technique is employed to characterize the behaviors of biomaterials. Nevertheless, there is a lack of development of a miniaturized precise positioner for in situ nanoindentation. Besides, modeling behaviors of the positioner are restricted due to its complex kinematic characteristics. Therefore, this paper proposes a novel compliant two degrees of freedom (dof) stage for positioning a biomaterial sample in in situ nanoindentation. In addition, a new modeling and dimensional optimization synthesis method of the stage is developed. The proposed effective methodology is developed based on a kinetostatic analysis-based calculation method, the Lagrange approach, and a neural network algorithm. With an increased advance in artificial intelligence, a neural network algorithm is proposed to extend the applicability of artificial neural networks in optimizing the parameters of the stage. First, the 2-dof stage is built via a combination of an eight-lever displacement amplifier and a symmetric parallelogram mechanism. Second, a chain of mathematical equations of the 2-dof stage is constructed using a kinetostatic analysis-based method to calculate the ratio of displacement amplification and the input stiffness of the 2-dof stage. Then, the Lagrange method is utilized to formulate the dynamic equation of the 2-dof stage. Finally, a neural network algorithm is adopted to maximize the natural first frequency of the proposed stage. The optimal results determined that the frequency of the stage can achieve a high value of 112.0995 Hz. Besides, the formed mathematical models were relatively precise by comprising the simulation verifications., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2022 Minh Phung Dang et al.)