Simple shear of end-tethered Nylon 6-clay nanocomposites and the preservation of these effects into the crystalline state is reported. Typical conditions leading to mesoscopic (clays) and molecular (polymer chains) orientation of these systems at relatively low shear rates and at temperatures immediately above the nominal melting point showed a morphological change proportional to the shear time in the molten state. Gradual alignment of the through-view SAXS patterns indicated the rotation of the end-tethered clay along the shear direction. High temperature relaxation of clay after shear was substantially longer than the polymer. Thus, non-isothermal crystallization into the crystalline state could be used to preserve the orientation of the clay induced by shear. It was found that most of the clay planar alignment in Nylon 6-clay nanocomposites rendered the gamma crystal habit, which is typically associated with the extended chain crystallization. Nylon 6, on the other hand, crystallized into the a habit commonly associated with quiescent crystals involving folded chains. The shear results were compared with quiescent crystallization, where the Nylon 6 nanocomposites exhibited the preferential gamma habit and the Nylon 6 homopolymer exhibited mixed alpha/gamma habits.