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Complete projection (360deg) free-space fluorescence tomography of opaque media is poised to enable 3-D imaging through entire small animals in vivo with improved depth resolution compared to 360deg-projection fiber-based systems or limited-view angle systems. This approach can lead to a new generation of fluorescence molecular tomography (FMT) performance since it allows high spatial sampling of photon fields propagating through tissue at any projection, employing nonconstricted animal surfaces. Herein, we employ a volume carving method to capture 3-D surfaces of diffusive objects and register the captured surface in the geometry of an FMT 360deg-projection acquisition system to obtain 3-D fluorescence image reconstructions. Using experimental measurements we evaluate the accuracy of the surface capture procedure by reconstructing the surfaces of phantoms of known dimensions. We then employ this methodology to characterize the animal movement of anaesthetized animals. We find that the effects of animal movement on the FMT reconstructed image were within system resolution limits (~0.07 cm).