In this paper, we propose a system to create high-precision maps using UAV-LiDAR and to determine the location of individual fruit trees (apple trees) on the maps. The system is based on a UAV-LiDAR system that flies over an actual orchard. A UAV was flown over an actual orchard, and the point cloud of the onboard LiDAR and the location information of RTK-GNSS were obtained. The system records the LiDAR point cloud and RTK-GNSS position information. Automated software processes point cloud data offline and Automated software processes point cloud data offline and automatically segments each apple tree in the map. The RTK-GNSS position information is used for the segmented trees. The positional information obtained from RTK-GNSS was georeferenced to the segmented trees without using ground evaluation points. As a sample, location information was obtained from trees using the Quasi-Zenith Satellite System (QZSS) MICHIBIKI. The positional accuracy of the trees was evaluated using the positional information obtained from the Quasi-Zenith Satellite System MICHIBIKI as a reference. As a result, the alignment accuracy was sufficient to identify individual fruit trees.