This work presents the development and application of a visualization and navigation system for planning deep-brain neurosurgeries. This system, which incorporates a digitized and segmented brain atlas, an electrophysiological database, and collections of final surgical targets of previous patients, provides assistance for non-rigid registration, navigation, and reconstruction of clinical image data. The fusion of standardized anatomical and functional data, once registered to individual patient images, facilitates the delineation of surgical targets. Our preliminary studies compared the target locations identified by a non-expert using this system with those located by an experienced neurosurgeon using regular technique on 8 patients who had undergone subthalamic nucleus (STN) deep-brain stimulations (DBS). The average displacement between the surgical target locations in both groups was 0.58 mm +/- 0.49 mm, 0.70 mm +/- 0.37 mm, and 0.69 mm +/- 0.34 mm in x, y, and z directions respectively, indicating the capability of accurate surgical target initiation of our system, which has also shown promise in planning and guidance for other stereotactic deep-brain neurosurgical procedures.