Low-frequency Raman spectra are performed on silver nanocrystals self-organized on a hexagonal compact array on highly oriented pyrolytic graphite (HOPG) substrate. In addition to the well-known Raman scattering by the nanoparticle quadrupolar vibration mode, two lower intensity bands at larger frequency shifts are observed. They are attributed to acoustic phonons confined in the nanocrystals corresponding to the fundamental breathing mode and its first harmonic. Their observation was made possible because of the high crystallinity and the narrow size distribution of the silver nanoparticles. The coated particles organized in 2D superlattices appear thus to behave as isolated particles dispersed in matrix.