We describe a method for plasma cleaning silicon surfaces in a commercial tool that removes adventitious organic contamination and enhances silane deposition. As shown by wetting, ellipsometry, and XPS, hydrogen, oxygen, and argon plasmas effectively clean Si/SiO2 surfaces. However, only hydrogen plasmas appear to enhance subsequent low-pressure chemical vapor deposition of silanes. Chemical differences between the surfaces were confirmed via (i) deposition of two different silanes: octyldimethylmethoxysilane and butyldimethylmethoxysilane, as evidenced by spectroscopic ellipsometry and wetting, and (ii) a principal components analysis (PCA) of TOF-SIMS data taken from the different plasma-treated surfaces. AFM shows no increase in surface roughness after H-2 or O-2 plasma treatment of Si/SiO2. The effects of surface treatment with H-2/O-2 plasmas in different gas ratios, which should allow greater control of surface chemistry, and the duration of the H-2 plasma (complete surface treatment appeared to take place quickly) are also presented. We believe that this work is significant because of the importance of silanes as surface functionalization reagents, and in particular because of the increasing importance of gas phase silane deposition.