An experimental instrument was made for the end-point detection of a deep small hole milled in large scale integrated circuit using focused ion beam (FIB). The SCANIIR method using photon-counting technique is adopted for detecting a very weak photoemission. The objective lens and imaging lens made by a quartz single lens are arranged in a parallel beam configuration. Observing optics, XY stage and Z controlling mechanism for the optics are also used. To avoid the noise from the wall of the hole, a blanking circuit for detected signals was used. Experiments using a wide angle objective optical system showed an aluminum layer lower than 10 mu m and the SiO2 layer below were able to be clearly discriminated.