A section processing apparatus has a mark forming control portion that transmits control information for forming marks on a surface of a sample. Each of the marks has at least two portions intersecting at a converging portion located at a previously determined position of an observation target section of the sample or in the vicinity of the previously determined position. A first focused ion beam apparatus emits a first focused beam for forming each of the marks on the surface of the sample based on the control information transmitted by the mark forming control portion and for processing a section of the sample. The section of the sample is processed by scanning the first focused beam in parallel with the at least two portions of the marks in the direction of the converging portion, while the section of the sample and positions of the marks are observed by a second focused ion beam apparatus, and to finish processing of the section of the sample when the first focused beam reaches the converging portion or a vicinity thereof.