Tip-enhanced Raman spectroscopy (TERS) is a powerful tool for nondestructive and label-free surface chemical characterization at nanometer length scales. However, despite being considered nondestructive, the interaction of the TERS probe used in the analysis can alter the molecular organization of the sample. In this study, we investigate the role of the atomic force microscopy (AFM) feedback (contact mode and tapping mode) on molecular perturbation in TERS analysis of soft samples using a self-assembled monolayer (SAM) of 2-chloro-4-nitrobenzene-1-thiol (Cl-NBT) as a test sample. Surprisingly, the tapping mode shows a consistently higher TERS signal resulting from a minimal perturbation of the Cl-NBT SAM compared to the contact mode. This study provides novel insights into the choice of the correct AFM-TERS operation mode for nanoscale chemical analysis of soft and delicate samples and is expected to expedite the growing application of TERS in this area.