In all prior electromagnetic modeling studies of carbon nanotube (CNT) composites, the exact three-dimensional (3D) shape and spatial distribution of the CNTs in the composite were unknown. Therefore, simplifying assumptions had to be made regarding the CNT distributions. The effect of such assumptions on the electromagnetic response of CNT composites has not been quantified. Recent advances in electron-tomography and image analysis have allowed the generation of 3D maps of multi-walled carbon nanotube (MWCNT) distributions with sub-nanometer resolution. In this work, the electromagnetic responses of experimentally mapped 3D structures of aligned-CNT polymer nanocomposites were calculated using both full-wave electromagnetic solvers and dilute-limit Effective Medium Approximations (EMA). Our results show that the electromagnetic response calculated using the full-wave solver exhibits additional resonances that are absent in the response calculated using the dilutelimit EMA. This difference is due to the strong electromagnetic coupling between adjacent MWCNTs, within five CNT radii, of each other. Using the mapped 3D MWCNTs, we also studied the anisotropy in the electromagnetic response of the composites and showed that it increases with the MWCNT volume fraction. The full-wave analysis presented in this work provides a more accurate understanding of the electromagnetic reflection and anisotropy of CNT composites.