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In this work ultrahigh-vacuum scanning tunneling microscopy (STM) is used to investigate ultrathin oxide films grown thermally by in situ dry oxidation of clean highly B-doped Si(100) substrates. On a clean starting surface, STM images reveal a special reconstruction induced by boron accumulation. The step structure of the substrate persists and can be recognized on the ultrathin oxide films, indicating layer-by-layer oxidation. The surface roughness is observed to increase upon oxidation, showing what appears in the STM image (at certain bias voltages) as both bright spots and dark holes. These oxidation-induced features also affect the formation of void structures when the oxide films are heated up to 700–750 °C. At the early stage of oxidation on the clean substrates, it is found that boron-induced reconstruction may have an effect on the formation of missing-dimer defects. © 2000 American Vacuum Society.