Target location accuracy is a key index for the microbeam irradiation. Therefore, a method for capturing and locating the microbeam position is offered. The microbeam position is identified by imaging the fluorescent spot excited when particles hit the scintillation foil. Using the image capture and analysis system, the fluorescent spot is analyzed to determine the microbeam position. Furthermore, experiments using CR39 nuclear track detector to measure the microbeam locating method are presented. The overall target location accuracy is measured when a borosilicate glass capillary with 5 μm inner diameter and 980 μm length is used as the microbeam collimator.