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Contact mode Atomic Force Microscopy (CM-AFM) is popularly used by the biophysics community to study mechanical properties of cells cultured in petri dishes, or tissue sections fixed on microscope slides. While cells are fairly easy to locate, sampling in spatially heterogeneous tissue specimens is laborious and time-consuming at higher magnifications. Furthermore, tissue registration across multiple magnifications for AFM-based experiments is a challenging problem, suggesting the need to automate the process of AFM indentation on tissue. In this work, we have developed an image-guided micropositioning system to align the AFM probe and human breast-tissue cores in an automated manner across multiple magnifications. Our setup improves efficiency of the AFM indentation experiments considerably.