Atomic force microscopy measurements are carried out on the surface and interface of SiO2 thermally grown on an atomically flat Si surface, and the uniformity of thickness on an atomic scale is investigated. Protuberances on the surface of SiO2 grown at 800 °C in 3.8 % O2 diluted by argon at the atmospheric pressure are generated in the initial stage of oxidation and subsequently increases in height at the same positions. The surface RMS value of SiO2 linearly increases up to the thickness of approximately 5 nm, which almost corresponds to what was called the initial oxidation thickness. This fact indicates that the roughness increase is related to the re-oxidation of SiO emitted from the Si/SiO2 interface during the initial oxidation. Additionally, the surface RMS value is saturated at a value of approximately 0.13 nm. A correspondence between the position of the dimples on the surface and the positions of the protuberances at the interface is also clear. The fact is the direct evidence of the local thinning of the thermally grown SiO2 films. Based on these results, an atomic scale thermal oxidation mechanism is discussed.