In this paper we present preliminary results obtained for tissue-like phantoms and ex vivo tissue slabs using a prototype system for CW infrared fluorescence imaging of fluorescent markers. Besides the design of the experimental system itself, we have developed a theoretical model of photon migration under experimental conditions and associated 3D reconstruction algorithms to estimate the distribution of fluorescent markers. Application of the developed algorithms in the analysis of 2D intensity distributions of the fluorescent light demonstrated their ability to reconstruct positions of the markers (including their depths) with good accuracy (error < or = 10%) both for the Intralipid phantoms and ex vivo tissue slabs.