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. In general, nanostructures and nanostructured materials have a much lower 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 with available experimental measurements. The thermal conductivity of a serie of phononic like crystals and parameters like neck distance, hole diameter, amorphisation of pores and spatial distribution of pores, as well crystalline/amorphous nanocomposites, 2D and 3D nanowires networks, the effect of dislocations and the radial heat flux in nanowires will be discused. The purpose is to appraise the impact of surface roughness, amorphous phase integration, diameter modulation as well growth direction on the thermal conductivity reduction.