An atomic layer polishing method is described. The method includes: scanning the surface of a specimen to measure a peak site on the specimen surface; spraying toward the measured peak site a gas containing an element capable of binding to a first atom, which is an ingredient of the material of the specimen to form a first reaction gas layer in which the first reaction gas binds to the first atom on the surface of the peak; and projecting ions of inert gas to the peak site on which the first reaction gas layer is deposited to separate the first atom bound to the first reaction gas from the specimen.