GaAs surface cleaning by thermal oxidation and sublimation prior to molecular‐beam‐epitaxial growth has been investigated as a means of reducing the carrier depletion at the substrate and epitaxial layer interface. The carrier depletion between the substrate and epitaxial films, measured by aC‐Vcarrier profiling technique, was shown to decrease significantly with an increase in the thickness of the thermal oxidation. The concentration of carbon contamination near the substrate‐epitaxial interface was measured using secondary ion mass spectroscopy. The carbon concentration correlated very well with the carrier depletion. Therefore, the main origin of the carrier depletion is believed to be the carbon concentration of the initial growth surface. Based on these results, the thermal oxidation and sublimation of a semi‐insulating GaAs substrate was successfully applied to improve the mobility and sheet concentration of the two‐dimensional electron gas in selectively doped GaAs/N‐Al0.3Ga0.7As heterostructures with very thin GaAs buffer layers.