We have studied by atomic force microscopy (AFM) the surface morphology of SiO2 layers grown by thermal oxidation of silicon wafers implanted with As, B, Ge, or Si ions. In order to grow oxides having comparable thickness at different temperatures, we have employed both dry and wet processes. Roughness values up to 0.4 nm have been measured on the surface of these oxides. Surface morphology is not influenced by the oxidation ambient, while temperature-related effects are predominant. For low temperature oxidation (920 degrees C), the predominating effects are due to the behavior of the implanted species, and mainly consist in segregation phenomena, that are the result of a complex competition among different factors, including the segregation coefficient, the relative diffusion rates in the oxide and silicon, and the oxidation rate. At higher temperature (1100 degrees C), impurity segregation is inhibited or considerably reduced by the increased diffusivity, and defects formation, due to the evolution of the radiation damage, becomes the main effect. Finally, the comparison among AFM, Rutherford backscattering spectrometry, and transmission electron microscopy data has allowed to demonstrate that the morphologies of the SiO2 surfaces are tightly related to the corresponding SiO2/Si interfaces.