Atomic force microscopy (AFM) has been employed to study the adsorption of alkyl- and (perfluoroalkyl)-trichlorosilane molecules on silica substrates. The effect of surface coverage on the packing of these long chain molecules and the rate of formation of the monolayers on the silica have been investigated and the results compared with those from Fourier transform infrared spectroscopic experiments. It was found that at low coverage of the silanes on the substrate island formation occurred and that as coverage approached monolayer the islands in the AFM images were in-filled to produce a smooth surface. Above monolayer coverage it has been found that disordered molecular islands were formed. These were not easily detected using FTIR but were clearly identified by AFM.