With the rapid evolution of materials elaboration a serie of nanostructures and nanostructured material like phononic-like crystals or nanowire networks and nanocomposites are easily fabricated today. In general, decreasing dimensionalities of materials drives to the decrease of their thermal conductivity compared to their bulk state, due to phonon confinement and boundary scattering. New physical phenomena are observed in such structures as ballistic phonon transport, phonon focusing, phonon tunneling, coherence effects, thermo-hydo-dynamic flow, etc. Such phenomena will be presented in several nanometric systems mainly extracted from Molecular Dynamics Simulations and in some cases compared with available experimental measurements. Here, several structures will be discussed as phononic like crystals, crystalline/amorphous nanocomposites, 2D and 3D nanowires networks (figure). The purpose is to appraise the impact of surface roughness, amorphous phase integration, diameter modulation as well growth direction on the thermal conductivity.