Silicon oxide surface properties can be easily modified by grafting alkoxysilane molecules. Here, we studied the structure and the morphology of ultrathin layers prepared by the grafting of alkoxysilanes having different head groups (thiol, amine, and iodo) in supercritical carbon dioxide (CO2) on model plane silicon oxide surfaces. Several characterization techniques (X-ray reflectivity, water contact angle, X-ray photoelectron spectroscopy, and atomic force microscopy (AFM)) were used to determine the physicochemical properties of the layers prepared at different temperatures. Moreover, for the first time, AFM peak force measurements were used to delve deeper into the determination of the structure of these ultrathin alkoxysilane layers. The results show that the grafting temperature and the nature of the head group strongly affect the morphology and structure of the grafted layers. Dense monolayers are obtained with 3-(mercaptopropyl)trimethoxysilane at 60 °C, polycondensed layers are always prepared with [3-(aminoethylamino)propyl]trimethoxysilane, and a dense bilayer is synthesized with 3-(iodopropyl)triethoxysilane at 120 °C.