We discuss the design and implementation of a novel multimodal coherent anti-Stokes Raman scattering (CARS) miniaturized microscope for imaging of injured and recovering spinal cords in a single living animal. We demonstrate for the first time, the use of a biaxial microelectromechanical system (MEMS) mirror for scanning and diffraction limited multiple lens miniaturized objective for exciting a CARS signal. The miniaturized microscope design includes light delivery using a large mode area photonic crystal fiber (PCF), and multimode fiber for collection of the nonlinear optical signal. The basic design concept, major engineering challenges, solutions, and preliminary results are presented. We demonstrate CARS and two photon excitation fluorescence microscopy in a benchtop setup with the miniaturized optics and MEMS scanning. The light source is based on a single femtosecond laser (pump beam) and a supercontinuum generated in a nonlinear PCF (Stokes beam). This is coupled using free space optics onto the surface of a resonantly driven two dimensional scanning MEMS mirror that scans the excitation light in a Lissajous pattern. The novel design of the miniaturized microscope is expected to provide significant new information on the pathogenesis of demyelinating diseases such as Multiple Sclerosis and Spinal Cord Injury.© (2011) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.