The success of stereotactic surgery for Deep Brain Stimulation depends critically on the exact positioning of a microelectrode recording in a target area of the brain. This paper presents the software system NEUROZONE composed of two main applications: first, it allows online recognition of brain structures by the analysis of signals from microelectrode recordings (MER), and second, it processes and analyses off-line databases allowing the inclusion of new trained classifiers for automatic identification. The software serves as a support to the analysis done by a medical specialist during surgery, and seeks to reduce the adverse side effects that may occur because of inadequate identification of the target areas. The software also allows the specialists to label recordings obtained during surgery, in order to generate a new off-line database or increase the amount of records in an already existing off-line database. NEUROZONE has been tested for Deep Brain Stimulation performed at the Institute for Epilepsy and Parkinson of the Eje Cafetero (Colombia), achieving positive identifications of the Subthalamic Nucleus (STN) over to 85% using a naive Bayes classifier.