1. A focused ion beam apparatus comprising: a sample stage configured to place a sample thereon and provided with a moving mechanism configured to move the position of the sample; a focused ion beam irradiating mechanism configured to irradiate the sample with a focused ion beam; a detector configured to detect a secondary charged particle generated from the sample when being irradiated with the focused ion beam or other electron beams; an image generating unit configured to generate an sample image of the sample on the basis of the detected data detected by the detector; a display unit configured to display the sample image; a processing area setting unit configured to set a processing area image including a plurality of pixels corresponding to positions to be irradiated with the focused ion beam on the sample image displayed on the display unit; a position of irradiation setting unit configured to set coordinates of the pixels included in the processing area image as the position to be irradiated on the sample; a beam setting unit configured to set a dose amount of the focused ion beam irradiated from the focused ion beam irradiating mechanism according to intensities predetermined on the pixel-to-pixel basis; and an interpolating unit configured to perform an interpolating process on the processing area image when the processing area image is deformed by the processing area setting unit.