In this paper, we report on the local thermal activation of thin polymer films for area-selective surface chemical modification on micrometer and nanometer length scales. The thermally induced activation of tert-butyl ester moieties in polystyrene-block-poly(tert-butyl acrylate) (PS-b-PtBA) block copolymer films leads to the formation of pending carboxylic acid groups, which are among the versatile functionalities for subsequent bioconjugation. From Fourier transform infrared (FTIR) spectroscopic analyses, the apparent activation energy (Ea) for the tert-butyl ester deprotection in thin films was calculated to be 93 ± 12 kJ/mol, which is in good agreement with values reported for the bulk. The availability of the deprotected carboxylic acid groups in subsequent wet chemical grafting reactions on neat thermolyzed films was confirmed by covalently immobilizing fluoresceinamine and amino end-functionalized poly(ethylene glycol) (PEG-NH2) using established 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC)/N-hydroxysuccinimide (NHS) chemistry. Local thermal deprotection on micrometer and sub-micrometer length scales was achieved by scanning thermal microscopy using an atomic force microscope with heatable probe tips. Passivating PEG and fluoresceinamine layers were selectively covalently coupled to locally deprotected areas as small as 370 nm × 580 nm.