The initiation of a corrosion process can be triggered by defects in the spatial distribution and molecular organization in the adsorbed layer of surfactant inhibitors. A detailed knowledge of the intermolecular forces between the inhibitor molecules and the interfacial bonding between the molecules and metal (oxide) surface will be decisive to unravel the mechanisms driving the initiation of corrosion and surface protection. In this work, adsorbed organic layers of two mercapto-based benzimidazole molecules, 5-methoxy-2-mercapto-benzimidazole (SH-BimH-5OMe) and 5-amino-2mercapto-benzimidazole (SH-BimH-5NH2) were studied regarding their inhibition performance of copper corrosion. Atomic force microscopy was used to address the stability and intermolecular forces of the self-assembled monolayers, using imaging and force measurement modes. For a film formed by amino derivative molecules, molecular fishing by a gold coated AFM tip frequently occurred. For molecular layers of the methoxy derivative, no fishing events were observed, indicating the formation of a constant functional performance layers. X-ray photoelectron spectroscopy revealed that SH-BimH-5OMe molecules form a stronger surface bond strength/interfacial bonding SAM layers on Cu surfaces as compared to SH-BimH-5NH2 molecules. Results of computational DFT modelling and electrochemical corrosion tests are in line with the AFM and XPS results.