Using a statistical -mechanics approach, we study the effects of geometry and entropy on the ordering of slender filaments inside non-isotropic containers, considering cortical microtubules in plant cells, and packing of genetic material inside viral capsids as concrete examples. Working in a mean -field approximation, we show analytically how the shape of container, together with self avoidance, affects the ordering of stiff rods. We find that the strength of the self-avoiding interaction plays a significant role in the preferred packing orientation, leading to a first-order transition for oblate cells, where the preferred orientation changes from azimuthal, along the equator, to a polar one, when self avoidance is strong enough. While for prolate spheroids the ground state is always a polar like order, strong self avoidance result with a deep meta-stable state along the equator. We compute the critical surface describing the transition between azimuthal and polar ordering in the three dimensional parameter space (persistence length, container shape, and self avoidance) and show that the critical behavior of this systems, in fact, relates to the butterfly catastrophe model. We compare these results to the pure mechanical study in [1], and discuss similarities and differences. We calculate the pressure and shear stress applied by the filament on the surface, and the injection force needed to be applied on the filament in order to insert it into the volume.