After a scan area for observing or processing a mask is set, a computer of the charged particle beam apparatus determines a plurality of scan lines in the scan area by the following steps of: setting a scan line along the outer circumference of the scan area; determining a scan line inside and along the thus set scan line; determining a scan line inside and along the thus determined scan line; and repeating the step of determining a scan line. After the scan lines are determined, the computer controls a scanning circuit to apply an ion beam to the scan lines while thinning out scan lines and/or pixels.