The micropatterning of two different photoactive target molecules, fluorescent quantum-dot nanocrystals and fluorescein, on quartz surface, immobilized through quartz-binding peptides was studied. The patterned substrates were examined using fluorescence microscopy to demonstrate the bifunctionality and the quality of the pattern fabrication. The experiment demonstrates the micropatterning of a functional target molecule conjugated to QBP1 onto a quartz surface using microcontact printing. The results of this indicates that the target molecule by itself has no affinity to quartz substrate. The biotinylated QBP as an ink, was also used, to generate a micropattern of a probe using microcontact printing. The results show that the attachment of quantum dots or photoactive molecules on a substrate is material-specific. The process described has a potential utility in the efficient problems or limitations associated with the conventional silane-based chemical methods.