Polymeric materials play an emerging role in biosensing interfaces. Within this regard, polymers can serve as a superior surface for binding and printing of biomolecules. In this study, we characterized 11 different polymer foils [cyclic olefin polymer (COP), cyclic olefin copolymer (COC), polymethylmethacrylate (PMMA), DI-Acetate, Lumirror 4001, Melinex 506, Melinex ST 504, polyamide 6, polyethersulfone, polyether ether ketone, and polyimide] to test for the applicability for surface functionalization, biomolecule micropatterning, and fluorescence microscopy approaches. Pristine polymer foils were characterized via UV-vis spectroscopy. Functional groups were introduced by plasma activation and epoxysilane-coating. Polymer modification was evaluated by water contact angle measurement and X-ray photoelectron spectroscopy. Protein micropatterns were fabricated using microcontact printing. Functionalized substrates were characterized via fluorescence contrast measurements using epifluorescence and total internal reflection fluorescence microscopy. Results showed that all polymer substrates could be chemically modified with epoxide functional groups, as indicated by reduced water contact angles compared to untreated surfaces. However, transmission and refractive index measurements revealed differences in important optical parameters, which was further proved by fluorescence contrast measurements of printed biomolecules. COC, COP, and PMMA were identified as the most promising alternatives to commonly used glass coverslips, which also showed superior applicability in subcellular micropatterning experiments.