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We report the characterization of metal-phthalocyanine (CuPc and CoPc) thin films prepared on magnetic substrates by spectroscopic ellipsometry (SE) and magneto-optical Kerr effect (MOKE) spectroscopy. CuPc films were prepared on lanthanum strontium manganite (LSMO) substrates while CoPc was deposited onto Co/Pt layer systems. We address the challenge to distinguish between the dominating magneto-optical response of the magnetic substrate and the contribution of the phthalocyanine layers. The procedure is demonstrated for CuPc on LSMO and also applied to CoPc on Co/Pt. The resulting spectral contribution of the organic films is compared to modeled spectra deduced from optical model calculations based on data previously obtained from phthalocyanines on silicon substrates. For CoPc on Co/Pt the average tilt angle of the molecular plane with respect to the substrate plane is estimated to be 73 ° from the ellipsometry data evaluation.