Most neuroscience research is performed by using anesthetized animals or tissue samples obtained from animals that have been euthanatized. However, study of many important issues requires the use of animals that are alert and capable of engaging in behavior. Various methods have been used to humanely perform neuroscience experiments that involved unanesthetized animals. These techniques often involve surgical implantation of an apparatus that permits direct manipulation of brain tissue or measurement of neurochemicals or neuronal activity in conscious animals. We describe here common surgical techniques used to prepare animals for long-term neuroscience studies, discuss several issues related to short- and long-term postoperative care of animals with implants, and offer suggestions that veterinary and research personnel can use to prevent or mitigate some common problems that may develop when preparing and maintaining animals for these studies.