The present invention relates to a surface treatment apparatus for cleaning or treating (micro etching, etc.) a surface of a TEM sample (substrate) by converting plasma ions into a neutral beam and a separator including an RF cathode connected to an RF supply unit and accelerating ions by self bias is disposed between a plasma generating chamber and a neutral chamber and the ions generated in the plasma generating chamber are converted into a neutral beam through a separator and accelerated and irradiated to a neutral chamber to enable surface treatment without damaging a sample.