Biodegradable polymers, such as Polycaprolactone (PCL), are receiving growing attention. The main limitation of PCL is its low stiffness regarding traditional polymers. The mechanical performance of PCL can be enhanced by the dispersion of nanometer-size inorganic particles such as clays (montmorillonite). In this work the effect of extrusion conditions on the performance of PCL/organo-modified clay nanocomposites was studied. It was demonstrated that the extrusion parameters have negligible effect on the molecular weight of PCL, on the morphology of the nanocomposites and on the final thermal/mechanical properties of these materials. This result was a consequence of the previous optimization of both polymer/clay compatibility and clay processing stability. In this work we propose another route to enhance the mechanical properties which is based on the following assumptions. It has been widely demonstrated that processing techniques such as film stretching produce the alignment of the polymer chains as a consequence of the induced extensional flow. Extensional flow is also present in injection molded parts but only on the vicinity of the mold wall. On the other hand, there are techniques such as compression molding which do not produce extensional flow. The hypothesis of this study is that the extensional flow that produces polymer chains alignment can also preferentially align clay platelets. It was found that despite the fact that the polymer/clay system with optimal polymer/clay compatibility and strongest clay organo-modifier processing stability was used, the mechanical properties of the nanocomposites could be further improve by clay platelets alignment induced by the different post-extrusion techniques. In the case of the nanocomposites prepared by film stretching, the clay alignment not only improved Young’s modulus but also the tensile strength of the nanocomposite without modifying the elongation at break.