Human fingerprints serve as one unique and powerful characteristic for each person, from which policemen can recognize the identity. Similar to humans, many natural bodies and intrinsic mechanical qualities can also be uniquely identified from surface characteristics. To measure the elasto-plastic properties of one material, one formally sharp indenter is pushed into the measured body under constant force and retracted, leaving a unique residual imprint of the minute size from several micrometers to nanometers. However, one great challenge is how to map the optical image of this residual imprint into the real wanted mechanical properties, i.e., the tensile force curve. In this paper, we propose a novel method to use multi-fidelity neural networks (MFNN) to solve this inverse problem. We first actively train the NN model via pure simulation data, and then bridge the sim-to-real gap via transfer learning. The most innovative part is that we use NN to dig out the unknown physics and also implant the known physics into the transfer learning framework, thus highly improving the model stability and decreasing the data requirement. This work serves as one great example of applying machine learning into the real experimental research, especially under the constraints of data limitation and fidelity variance.