Infrared vibrational spectroscopy in an attenuated total reflection geometry has been employed to investigate the presence of organic and inorganic thin layers on Si-wafer surfaces. Three different processes were compared for surface contaminant removal; microwave plasma, UV-ozone, and a piranha solution cleaning. The CH vibrations at 2928 and 2856 cm-1 characteristic of organic contaminants were monitored before and after each cleaning procedure to determine how well it removed surface contaminants. We found that native oxide removal from the Si surface should only be carried out after a cleaning essay. We observed that surface oxide removal exposed a hydrophobic bare Si surface, attracting organic molecules present in solution or the ambient. A large increase of the CH vibrational signature was observed for a Si wafer after an HF dip. A combination of plasma cleaning followed by UV-Ozone treatment was found the most effective one for Si wafer cleaning. We were able to evaluate the effectiveness of the cleaning methods, hydrogen surface passivation and oxide removal/regrowth.