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Action of ultra-short laser pulses on nanostructures opens the possibility of studying the physical processes occurring in them on ultrashort time scales. Thus, heating of metal nanofilms under the action of femtosecond laser pulses causes thermoelastic excitation of oscillations in terahertzs frequency range. Further propagation of acoustic pulses through layered nanostructures like photonic or phononic crystals can be used for development of new ultrafast nanophotonic and nanoacoustic devices due to excitation of high-frequency coherent changes in the thickness of layers. We present the results of numerical modeling of excitation of ultrafast vibrations in layered heterogeneous nanostructures due to absorption of the energy of ultrashort laser pulses. Heating of metal films is described in terms of two-temperature model for the electron gas and the ionic lattice. Spatio-temporal dynamics of excitation and propagation of acoustic waves is investigated by numerical solving the equations of motion of continuous media in the Lagrange form.