Fluorescence imaging is a powerful technique with diverse applications in intraoperative settings. Visualization of three dimensional (3D) structures and depth assessment of lesions, however, are oftentimes limited in planar fluorescence imaging systems. In this study, a novel Fluorescence Imaging Topography Scanning (FITS) system has been developed, which offers color reflectance imaging, fluorescence imaging and surface topography scanning capabilities. The system is compact and portable, and thus suitable for deployment in the operating room without disturbing the surgical flow. For system performance, parameters including near infrared fluorescence detection limit, contrast transfer functions and topography depth resolution were characterized. The developed system was tested in chicken tissues ex vivo with simulated tumors for intraoperative imaging. We subsequently conducted in vivo multimodal imaging of sentinel lymph nodes in mice using FITS and PET/CT. The PET/CT/optical multimodal images were co-registered and conveniently presented to users to guide surgeries. Our results show that the developed system can facilitate multimodal intraoperative imaging.