The presence of preferential organization of lamellar regions in the vicinity of soft (maleic anhydride grafted polyethylene-octene copolymer, POE-g-MA) and rigid (clay) nanofillers and how these interfaces or ligament regions between the nanoadditives and a polymer, polyamide-6, contribute toward the toughening processes were studied. The preferential lamellar orientation was observed only in the core region of the injection-molded polymer nanocomposites, while in other regions flow-induced crystallization was the controlling factor. In the case of soft fillers, it was shown that the orientation of transcrystalline lamellae along the tensile direction to promote shear yielding is a complex process, but it is not a predominant factor controlling the total toughness of the polymer blend, which is the sum of all the deformation processes occurring in all the regions (i.e., surface, intermediate, and core) of the injection-molded samples. For rigid clay systems, delamination of the clay layers occurred and resulted in only a slight increase of the toughness. Hence, it was suggested that without extensive matrix shear yielding activated by full debonding of the clay/matrix interfaces large improvements in toughness cannot be realized.