Semiconductor surface cleaning, passivation and functionalization are critical steps for applications such as microelectronics, MEMS, sensors, and solar energy harvesting. Progress has relied in part on the development of surface chemical treatments. However, the ability to characterize surfaces at all steps of processing has also been essential and will be emphasized here. This work focuses on the chemical modification of oxide-free, hydrogen-passivated silicon, including wet chemical treatments, atomic layer deposition, and physical deposition. Characterization methods include in-situ infrared absorption spectroscopy, low energy ion scattering, x-ray photoelectron spectroscopy and mass spectrometry, and is complemented by ex-situ spectroscopic ellipsometry and atomic force microscopy.