A study of the impact of the size and shape of a nanoparticle on the evolution of structure and surface segregation in polymer nanocomposite thin films is presented. This is realized by monitoring the evolution of structure with thermal annealing and equilibrium depth profile of a deuterated polystyrene/protonated polystyrene bilayer in the presence and absence of various nanoparticles. For the three shapes examined, sheet-like graphene, cylindrical carbon nanotubes, and spherical soft nanoparticles, the presence of the nanoparticles slowed the inter-diffusion of the polymers in the thin film. The larger nanoparticles slowed the polymer motion the most, while the smaller spherical nanoparticles also significantly inhibited polymer chain diffusion. At equilibrium, the soft spherical nanoparticles, which are highly branched, segregate to the air surface, resulting in a decrease in the excess deuterated PS at the surface. The graphene sheets and single walled carbon nanotubes, on the other hand, enhanced the dPS segregation to the air surface. The graphene sheets were found to segregate to the silicon surface, due to their higher surface energy. Interpretation of these results indicates that entropic factors drive the structural development in the nanocomposite thin films containing the spherical nanoparticles, while a balance of the surface energies of the various components (i.e. enthalpy) controls the thin film structure formation in the polymer-carbon nanoparticle nanocomposites.