When you have mentioned Si-wafer , I am considering you have selected an oxidized wafer (the surface is SiO2). How did you prepared the SiO2 surface , (how did you cleaned it before using it)?

I like this silanization method! I think Seyed is right-on, that the cleaning procedure is very important. When I used this method I prepped my wafers in piranha solution before silanizing. Also the trichlorosilane could be polymerizing from the surface ... can you use a dimethyl monochlorosilane instead?

Most of the salinization processes are based on the hydrolysis and condensation reaction between the Si-R (R=Cl, OCH3) and Si-OH, where water molecule is also attending the reaction in the salinization process. The inhomogeneous absorbed water molecules on the surface of the silicon wafer will induce the heterogeneous surface reactions leading inhomogeneous patterns on surface. Therefore, you can carry out the reaction ether in liquid phase (dissolve saline in solvent like toluene) or in vapor phase under elevated temperature in vacuum oven which will be helpful to obtain homogeneous salinization.