We have observed phonons diffraction and interference patterns at the atomic scale, using molecular dynamics simulations in systems containing crystalline silicon and nanometric obstacles as voids or amorphous-inclusions. The diffraction patterns caused by these nano-architectured hybrid systems of the same order as the phonon wavelengths are similar to the ones predicted by a simple Fresnel- Kirchhoff integral. These findings give evidence of the wave nature of phonons, can help to a better comprehension of the interaction of phonons with nanoobjects and at long term can be useful for intelligent thermal management and phonon frequency filtering at the nanoscale.