The UHV-prepared Si(100)-2×1:H surface is studied at atomic resolution following liquid phase chemical processing under atmospheric pressure conditions. A custom experimental setup, consisting of an UHV scanning tunneling microscope (STM) chamber that is directly interfaced to an inert atmosphere glovebox, facilitates liquid phase chemical processing without exposing the pristine H-passivated surface to ambient air. While in the inert atmosphere, the Si(100)-2×1:H surface is treated with a variety of organic and aqueous solvents. Atomic resolution STM images reveal that the hydrogen passivation remains largely intact after treatments in toluene and dichloromethane. In addition, by minimizing oxygen levels during processing, perturbation to the Si(100)-2×1:H surface can be significantly reduced following exposure to water. These results are potentially useful in the fields of microelectronics and molecular-beam epitaxy, where liquid phase chemical processing is often avoided in an effort to preserve atomically pristine Si(100) surfaces. Furthermore, this study delineates the conditions under which various organic and biological molecules can be delivered to nanopatterned Si(100)-2×1:H surfaces via liquid phase solvents. © 2004 American Vacuum Society.