Anatomical knowledge of target structures is essential in stereotactic functional neurosurgery. Thus, we created a three-dimensional(3D)atlas comprising frozen sections and histologically stained slides prepared from cadaveric brains. Herein, we describe the anatomical information of stereotactic functional neurosurgery targets gained from our atlas. The subthalamic nucleus(STN)was found to be clearly enclosed by neural fibers with high neuronal density. Based on our 3D models, the mean penetration length of deep brain stimulation leading into the STN was 6.6 mm. The globus pallidus was found to be clearly divided into the grobus pallidus externus(GPe)and internus(GPi)by its neural fibers, and the optic tract was located below the GPi. Although the thalamic lateral nuclear group(ventrooralis, ventrontermedius, and ventrocaudalis)could not be identified from either macroscopic frozen sections or MR images, these structures were clearly discernible from each other based on cell architecture(cell size and cell density)when viewed under a microscope. In contrast, distinguishing ventral and dorsal nuclei in humans is difficult. In addition to the main targets of the basal ganglia, we also investigated the anatomy of other targets in detail(posterior subthalamic area, pedunclopontine nucleus, nucleus accumbens, and nucleus basalis of Meynert). Overall, this anatomical knowledge from the atlas helps functional neurosurgeons interpret intraoperative microelectrode recording and MRI more precisely, helping facilitate more accurate surgeries.