When scanning by an ion beam in advance an area 24 including a reference hole 23 formed at a position other than the area to be processed 25 of a light-shielding film 21 on a glass substrate 22, a secondary ion signal of the same atom as the incident ions injected into the substrate is detected instead of detecting the secondary ion signal of the atoms included in the base film, and the position 23 of the hole is stored. Then, the area 24 including the hole formed during the processing is scanned and the secondary ion signal of the same atom as the incident ions is detected to determine the current position 26 of the hole, the position of the hole obtained by the previous detection and the current position of the hole are compared, and the amount of shift of the position of the hole is determined. This shifted amount is regarded as the drift amount.