In this paper, the Si(100) substrate was implanted by Ge ions at different doses to study the effect of the preliminary heat treatment on the wet oxidized layer of the Si using Rutherford Backscattering Spectroscopy and Atomic Force Microscopy. We found that the change of the silicon oxide thickness and its morphology under the influence of the Ge dopant is mostly dependent on the damaged surface layer of the Si substrate after ion implantation. By choosing different doses of the implantation and subsequent annealing process, we tried to get different level of the induced damage, enabled us to investigate the role of the pre-heating and subsequent recrystalization of the damaged substrate on the silicon oxidation process under the effect of the implanted Ge ions. By the determination of the effect of these parameters, we can better identify the optimal conditions of getting the oxide layer with proper thickness and morphology.