Photothermal patterning of poly(ethylene glycol) terminated organic monolayers on surface-oxidized silicon substrates is carried out using a microfocused beam of a CW laser operated at a wavelength of 532 nm. Trichlorosilane and trimethoxysilane precursors are used for coating. Monolayers from trimethoxysilane precursors show negligible unspecific protein adsorption in the background, i.e., provide platforms of superior protein repellency. Laser patterning results in decomposition of the monolayers and yields chemical templates for directed immobilization of proteins at predefined positions. Characterization is carried out via complementary analytical methods including fluorescence microscopy, atomic force microscopy, and scanning electron microscopy. Appropriate labeling techniques (fluorescent markers and gold clusters) and substrates (native and thermally oxidized silicon substrates) are chosen in order to facilitate identification of protein adsorption and ensure high sensitivity and selectivity. Variation of the laser parameters at a 1/e(2))spot diameter of 2.8 mu m allows for fabrication of protein binding domains with diameters on the micrometer and nanometer length scale. Minimum domain sizes are about 300 nm. In addition to unspecific protein adsorption on as-patterned monolayers, biotin-streptavidin coupling chemistry is exploited for specific protein binding. This approach represents a novel facile laser-based means for fabrication of protein micro- and nanopatterns. The routine is readily applicable to femtosecond laser processing of glass substrates for the fabrication of transparent templates.