An ultrahigh vacuum scanning microscopy has been applied to analyze wet-chemically prepared Si(001) surfaces in an atomic scale. The surface treated by 2.5% HF is atomically rough and is covered by featureless corrugations resulting from an etching by OH ions in the solution. The surface treated by HF:HCl = 1:19 mixed solution without controlling an oxide-removal direction is also atomically rough, but is characterized by a kinkful morphology, which reflects the crystallographic nature of the Si(001) surface. On the other hand, the surface treated by the same mixed solution but by controlling the oxide-removal direction is covered by regular monatomic steps and the ordered dihydride on the terrace. From these facts, we have confirmed that these factors, the concentration of the OH ions and the way of the oxide-removal, play roles in the preparation of the atomically flat Si(001) surface.