Thin microstructured poly(methyl methacrylate) (PMMA) films may be used as scaffolds for biosensor arrays. Microstructured pores form miniaturized vessels, each constituting an individual reaction vessel or detector element. Arrays of micropores with diameters between 2 and 80 μm were prepared in thin PMMA films on gold by optical lithography. Laterally resolved chemical information for microstructured PMMA films on a gold substrate was obtained by FTIR spectroscopic imaging. The carbonyl band was used to characterize the microstructure. Spectroscopic results indicate small amounts of PMMA residues inside the pores. A downshift of 5 cm^-1 compared to the position of the PMMA bulk carbonyl band indicates interactions of the PMMA residue with the gold substrate. Additional small bands are observed which indicate the formation of carboxylate during PMMA microstructuring. Three possible types of strong PMMA-gold interactions are discussed. All strong PMMA-gold interactions involve carbonyl or carboxyl oxygen.