A sample to be processed is disposed within a processing cell which contains a liquid. Scratch processing using a scanning probe microscope is performed within the liquid so that chips or shavings removed from the sample scatter within the liquid rather than collecting on the surface of the sample. The processing cell has a supply port and a discharge port so that new liquid can be supplied within the cell through the supply port after the termination of the scratch processing to clean the cell. In this manner, chips or shavings generated by scratch processing a defect portion of the sample can be removed completely without being collected at the surface of a sample despite the surface tension of adsorbed water existing on the sample surface and/or electrostatic charges caused by friction.