Nanobiocomposites are a new class of biodegradable polymer materials with an ultrafine phase dispersion of the order of a few nanometers in a biodegradable polymer matrix that shows very interesting properties often very different from those of conventional filled polymers. In this work the effect of the polarity of the organomodified montmorillonite and of the elongational flow on the morphology and the rheological and mechanical properties of a new nanobiocomposite having as a matrix a biodegradable copolyester based blend has been investigated. The morphology of the nanocomposite with the more polar organomodified clay shows a more exfoliated morphology due to the major compatibility with the polyesters of the matrix. This morphology leads to better mechanical properties. The same effect is given by the elongational flow applied to the two samples during a spinning test. The elongational flow induces a more relevant exfoliation in these samples due to the action of the gradient velocity on the platelets of the organomodified clay.