It has been demonstrated previously that infrared neural stimulation (INS) can be used to stimulate spiral ganglion cells in the cochlea. With INS, neural stimulation can be achieved without direct contact of the radiation source and the tissue and is spatially well resolved. The presence of fluids or bone between the target structure and the radiation source may lead to absorption or scattering of the radiation and limit the efficacy of INS. To develop INS based cochlear implants, it is critical to determine the beam path of the radiation in the cochlea. In the present study, we utilized noninvasive X-ray microtomography (microCT) to visualize the orientation and location of the optical fiber within the guinea pig and cat cochlea. Overall, the results indicated that the optical fiber was directed towards the spiral ganglion cells in the cochlea and not the nerve fibers in the center of the modiolus. The fiber was approximately 300 μm away from the target structures. In future studies, results from the microCT will be correlated with physiology obtained from recordings in the midbrain.