We have developed a three dimensional (3D) multispectral fluorescence optical tomography small animal imaging system with an innovative geometry using a truncated conical mirror, allowing simultaneous viewing of the entire surface of the animal by an EMCCD camera. A conical mirror collects photons approximately three times more efficiently than a flat mirror. An x-y mirror scanning system makes it possible to scan a collimated excitation laser beam to any location on the mouse surface. A pattern of structured light incident on the small animal surface is used to extract the surface geometry for reconstruction. A finite element based algorithm is applied to model photon propagation in the turbid media and a preconditioned conjugate gradient (PCG) method is used to solve the large linear system matrix. The reconstruction algorithm and the system feasibility are evaluated by phantom experiments. These experiments show that multispectral measurements improve the spatial resolution of reconstructed images. Finally, an in vivo imaging study of a xenograft tumor in a mouse shows good correlation of the reconstructed image with the location of the fluorescence probe as determined by subsequent optical imaging of cryosections of the mouse.