Background: Many current neuroscience studies in large animal models have focused on recordings from cortical structures. While sufficient for analyzing sensorimotor systems, many processes are modulated by subcortical nuclei. Large animal models, such as nonhuman primates (NHP), provide an optimal model for studying these circuits, but the ability to target subcortical structures has been hampered by lack of a straightforward approach to targeting. New Method: Here we present a method of subcortical targeting in NHP that uses MRI-compatible titanium screws as fiducials. The in vivo study used a cellular marker for histologic confirmation of accuracy. Results: Histologic results are presented showing a cellular stem cell marker within targeted structures, with mean errors ± standard deviations (SD) of 1.40 ± 1.19 mm in the X-axis and 0.9 ± 0.97 mm in the Z-axis. The Y-axis errors ± SD ranged from 1.5 ± 0.43 to 4.2 ± 1.72 mm. Comparison with existing methods: This method is easy and inexpensive, and requires no fabrication of equipment, keeping in mind the goal of optimizing a technique for implantation or injection into multiple interconnected areas. Conclusion: This procedure will enable primate researchers to target deep, subcortical structures more precisely in animals of varying ages and weights.