A processing method uses a probe of a scanning probe microscope. A fine marker is formed in a processing material by thrusting the probe, which is made of a material harder than the processing material, into a portion of the processing material disposed in the vicinity of an area of the processing material to be processed by the probe during a processing operation. A position of the fine marker on the processing material is detected during the processing operation. A drift amount of the area of the processing material is calculated in accordance with the detected position of the fine marker. A position of the area of the processing material is corrected in accordance with the calculated drift amount.