BACKGROUND Fast, effective, and rapid processing of central nervous system (CNS) tissue with good preservation of myelin, especially in tissue from diseased mice, is important to many laboratories studying neurosciences. METHODS In this paper, we describe a new method to process and embed CNS tissue from mice. Spinal cords and optic nerves from naive C57BL/6 mice were used to standardize the microwave protocol following perfusion with fixative. The CNS tissue was processed and embedded using the microwave embedding protocol. RESULTS We observed that the tissue is well preserved and good quality light and electron microscope images were obtained after using the microwave embedding protocol. METHODS Traditional way of embedding CNS tissue in resin is challenging and time consuming. The microwave technology offers an efficient way to quickly embed CNS tissue while preserving morphology and retaining the integrity of the myelin. CONCLUSIONS This new method is fast, reliable and an effective way to embed CNS tissue in resin.