The electronic structure of the central iron ion of perfluorinated iron phthalocyanine (FePcF16) in thin films has been studied on Cu(111) and Ag(111) using polarization dependent X-ray absorption spectroscopy (XAS). The data are compared to FePc on Ag(111). Ligand field parameters have been computed, and multiplet calculations (CTM4XAS) were carried out to simulate XAS spectra. The planar molecules are preferentially oriented lying flat on the substrate surface during the growth of the 1-4 nm thick films. A clear polarization dependence of the Fe L edge absorption spectra is observed, arising from transitions into orbitals with in-plane and out-of-plane character. The shape of the spectra for three to four monolayers of FePcF16 on Cu(111) is comparable to that of the thin films of FePc on Ag(111). However, a drastic change of the XAS peak shape is observed for thicker FePcF16 films on both Ag(111) and Cu(111), although the molecular orientation is very similar to coverages consisting of a few monolayers. Since in both cases the film thickness is distinctly beyond the monolayer regime, interface interactions can be ruled out as a possible origin of this behavior. Rather, the different XAS peak shapes seem to indicate that the multiplicity may depend on the detailed arrangement of the FePcF16 molecules. The large flexibility of the ground state of Fe could be of high interest for spintronic applications.