Several factors affect the interlaminar shear strength of carbon nanotube reinforced carbon fiber composites in multi-scale. A combined route of CNT toughening through manufacturing a custom made prepreg system with CNT dispersion in epoxy and integrating vertically aligned CNTs as nanofibers to bridge in between prepreg plies is applied to achieve enhanced interlaminar shear strength (ILSS). Depending on the CNT loading, effectiveness of dispersion and CNT bridging between prepreg plies, the mechanical enhancement is achieved up to 15%. A new approach of identifying the critical parameters of nano-engineered and nano-reinforced composites through Taguchi method is a novel route for investigating the combined effects of several factors in a complex mechanical enhancement problem with reduced number of experiments as studied in here. Taguchi L8 orthogonal array is used to obtain maximum ILSS by short beam shear (SBS) test. The parametric study has shown that the most significant parameters affecting the ILSS results are type of epoxy, fabrication procedure and CNT loading.