This paper investigates the doping of CVD-grown graphene transferred onto a SiO2/Si substrate, considering the effects of substrate preparation treatments (before the transfer) and thermal annealing processes of transferred graphene (to remove PMMA residues). The effect of post-transfer annealing on the doping of graphene was investigated by measuring the changes in the sheet resistance, mobility, and carrier density at 200 and 550°C in vacuum conditions. The Five different pre-treatments of the SiO2 surface, i.e., using solvents (acetone and IPA, piranha, HF), spin-coating with HMDS, and O2 plasma, were investigated to modify the hydrophobic or hydrophilic character of the SiO2 surface. Then the effects of substrate hydrophilicity on the amount of transferred graphene cavity and doping before and after annealing were studied according to the electrical resistance and shift and intensity ratios of the graphene Raman peaks (D, G, and 2D).