We examined the surface of a YBa₂Cu₃O_x (YBCO) single crystal by an atomic force microscope (AFM) in order to use the surface as a substrate for homoepitaxial growth. A step-and-terrace feature was revealed on the YBCO (001) surface after mechanical polishing, however YBCO at the topmost layer showed an unusual c-axis length (appeared in step height) much greater than normal one in precise AFM observations. Instability of the surface at high temperatures and poor reproducibility of homoepitaxial films obtained were caused by this degraded YBCO layer. The damaged layer was removed by the chemical etching using HCl/methanol solution. This treatment brought a topmost surface of YBCO single crystal, which made it possible to grow homoepitaxial YBCO films reproducibly.