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Photo-induced Force Microscopy (PiFM) is a nanoanalytical, surface-sensitive new-frontier technique that provides infrared spectroscopy for molecular imaging at a spatial resolution of ~5 nm 2 , approximately one billion times higher than traditional FTIR. These advantages have led to significant discoveries in earth and environmental sciences, as well as related disciplines. However, the high resolution and surface sensitivity of PiFM also make it highly susceptible to surface contamination. Factors such as sample preparation, handling, and storage can introduce particulate and/or molecular contaminants which may interfere with data analysis and lead to misinterpretation of results. In this study, we systematically investigate common laboratory materials, including gloves, mounting materials, polishing agents, and storage solutions as potential sources of particulate and molecular contaminants, which we present as a library of reference spectra available to all users of nano-scale molecular analyses. Further, we determined the contaminant signatures of human skin and gloves on AFM substrates and provide recommendations for sample preparation, handling, and storage as well as strategies for contamination mitigation to ensure better informed analysis of structurally and compositionally complex geological materials. By identifying molecular and particulate contaminants through their specific IR absorption bands, and selectively avoiding or removing them, we improve the reliability and confidence of nanoscale molecular analyses by PiFM, ultimately increasing confidence in new discoveries.