Protein microarrays are established as powerful tools for protein detection, probing their expression, and studying protein interactions. It was the object of this project the development of a novel method for fabrication of protein microarrays on Si or polymeric substrates, based on protein spotting in combination with chemical and/or topographical modification of selected areas of the chip. The project aimed at the creation of protein spots with diameter of the order of 1 μm, i.e. of density much higher than the one allowed by the current commercial instruments for protein spotting. This was achieved by the preparation of “smart” substrates, patterned and modified chemically (in the scale of 1 μm) and topographically (in the nanoscale), on which multiple protein spots of 1 μm in diameter can be printed in one step. For the chemical modification, we proposed the selective deposition of fluorocarbon films only on areas of appropriate composition, so as to determine the areas of selective protein deposition. As such substrate surfaces, we proposed SiO₂ and a widespread polymer, polydimethylsiloxane ([Si(CH3)2-O]n).