In this article, we present temperature and orientation study of iron phthalocyanine (FePc) thin films with different thickness deposited on silicon substrate. The organic thin films were obtained by the quasi-molecular beam evaporation. The micro-Raman scattering spectra of FePc thin layers were investigated in the spectral range 550-1,800 cm -1 using 488-nm excitation wavelength. The Raman scattering and atomic force microscopy studies were performed at room temperature before and after annealing process. Annealing process of thin layers was carried out at 453 K for 6 h. From polarized Raman spectra using surface Raman mapping procedure the information on distribution of polymorphic phases of FePc layers has been carried out. Moreover, the obtained results showed the influence of the annealing process on the ordering of the molecular structure of thin films deposited on silicon substrate. For the very thin layers we did not observe the change of the polymorphic phase but only reordering of the thin layers and change of molecular structure to intermediate phase. Using atomic force microscopy method, we observed arrangement of the thin layers structure connected with the change of roughness of the thin layers after annealing process. The obtained results indicate that the structure of thin layer deposited on silicon substrate is strongly affected by the annealing process.