The vibrational properties of single-layer PTCDA (perylene-3,4,9,10-tetracarboxylic dianhydride) and H2Pc (metal-free phthalocyanine) thin films and PTCDA-H2Pc double-layer heterostructures are studied by Raman scattering. The evidence of crystallinity of the single-layer films can be supported by the existence of phonons, as well as polarization dependence. Resonance enhancement Raman scattering has been used to selectively measure the individual layer properties in double-layer H2Pc/PTCDA and PTCDA/H2Pc heterostructures. When H2Pc is grown on PTCDA, its structure departs from the herringbone arrangement characteristic of unstrained H2Pc films, as demonstrated by the different peak intensities in the Raman spectra. Well-defined phonons and the polarization dependence in the H2Pc top layer are characteristic of long-range order, indicating that the H2Pc molecular planes in the templated structure are crystalline. No evidence for a new structure was observed for PTCDA deposited on top of a H2Pc first layer. Here, the relative intensity of the phonons in the PTCDA top layer demonstrates that the PTCDA forms microcrystallites due to strain at the molecular heterojunction, before relaxing to its bulk crystalline form.