We have demonstrated oxidation of the spatially controlled atomically flat Si(001) surface by exposing O 2 gas, and investigated morphologies of the SiO 2 surface and the SiO 2 /Si(001) interface using atomic force microscopy. When the O 2 pressure was low at high substrate temperatures (>400 o C), anisotropic surface etching occurred. Monoatomic-deep pits elongated in the direction of the dimer rows were formed on the Si(001) terraces. Thus, the O 2 exposure resulted in the roughening of the atomically flat Si(001) surface. When the O 2 pressure was kept high at the high substrate temperatures on the other hand, the oxidized specimens were free from the etching and had good morphologies at the SiO 2 surface and the SiO 2 /Si(001) interface, whose root-mean-square values of roughness are small compared with a monoatomic-step-height.