Stereotactic neurosurgery and neurophysiological microelectrode recordings in both humans and monkeys are typically done with conventional 2D atlases and paper records of the stereotactic coordinates. This approach is prone to error because the brain size, shape, and location of subcortical structures can vary between subjects. Furthermore, paper record keeping is inefficient and limits opportunities for data visualization. To address these limitations, we developed a software tool (Cicerone) that enables interactive 3D visualization of co-registered magnetic resonance images (MRI), computed tomography (CT) scans, 3D brain atlases, neurophysiological microelectrode recording (MER) data, and deep brain stimulation (DBS) electrode(s) with the volume of tissue activated (VTA) as a function of the stimulation parameters. The software can be used in pre-operative planning to help select the optimal position on the skull for burr hole (in humans) or chamber (in monkeys) placement to maximize the likelihood of complete microelectrode and DBS coverage of the intended anatomical target. Intra-operatively, Cicerone allows entry of the stereotactic microdrive coordinates and MER data, enabling real-time interactive visualization of the electrode location in 3D relative to the surrounding neuroanatomy and neurophysiology. In addition, the software enables prediction of the VTA generated by DBS for a range of electrode trajectories and tip locations. In turn, the neurosurgeon can use the combination of anatomical (MRI/CT/3D brain atlas), neurophysiological (MER), and electrical (DBS VTA) data to optimize the placement of the DBS electrode prior to permanent implantation.