Due to the rapid evolution of nanomaterials elaboration the last decade a serie of nanostructures and nanostructured material like phononic-like crystals or nanowire networks are easily fabricated today. New physical phenomena are observed in such structures as ballistic phonon transport, phonon focusing, phonon tunneling and coherence effects. In general, nanostructured materials have a much lower thermal conductivity compared to bulk materials, due to phonon confinement and boundary scattering. Such phenomena will be presented with the present work. The thermal conductivity of a serie of structural, diameter, core/shell modulated and growth direction of silicon, silicon carbite and bismuth telluride nanowires and phononic like crystals and parameters like neck distance, hole diameter, amorphisation of pores and filling of a second type of material will also be presented using atomistic and mesoscopic simulations. The purpose is to appraise the impact of surface roughness, amorphous parts integration, diameter modulation as well growth direction on the thermal conductivity reduction. The addition of both amorphous regions and nanoconstrictions hinder the thermal conductivity even under the amorphous limit, while preserving a large crystalline volume fraction.