A gradient charged particle beam apparatus capable of moving highly accurately to a specific position by eliminating influences of warp inside a wafer surface is provided. A portion 46 having a mark 47 for aligning visual field alignment positioned in advance to the same horizontal and the same height as a stage plane as a reference point is arranged on a wafer holder. A height of an observation point on a sample is adjusted to the height of the mark 47 and the visual field of a gradient column is brought into conformity with the visual field of a vertical column by use of a known offset between the gradient column and the vertical column at that time.