A composite beam apparatus includes an electron beam column for irradiating an electron beam onto a sample, a focused ion beam column for irradiating a focused ion beam onto the sample to form a cross section, and a neutral particle beam column having an acceleration voltage set lower than that of the focused ion beam column for irradiating a neutral particle beam onto the sample to perform finish processing of the cross section. The electron beam column, the focused ion beam column, and the neutral particle beam column are arranged such that the beams of the columns cross each other at an irradiation point. A controller controls the electron beam column to irradiate and scan the electron beam on the sample during cross section processing by the focused ion beam column and during finish processing by the neutral particle beam column. The composite beam apparatus is capable of suppressing the influence of charge build-up, or electric field or magnetic field leakage from an electron beam column, when subjecting a sample to cross-section processing with a focused ion beam and then performing finishing processing with another beam.