The changes in morphology and chemical states of Si(100) surface upon dipping in ultrapure water were investigated by using X-ray photoelectron spectroscopy and atomic force microscope. In ultrapure water, the oxidation and the etching competitively progressed at the Si(100) surface after HF treatment and made the smooth surface rough. However, the surface covered with a thick native oxide film was not etched at all. That meant the precise Si 4+ component remained without being etched, whereas rest parts of the surface could be etched. This selective etching led to the rough surface morphology. O − and OH − ions might take oxidizing and etching at the surface after HF treatment.