We describe an adaptation of the microcontact printing technique for generating self-aligned patterns of two different molecules in one printing step. Elastomeric stamps exhibiting different levels of topography are designed and fabricated so that, by external pressure, their deformation enables two planes, selectively inked with two different molecules, to contact the surface. The fabrication of 1 mu m wide biomolecular patterns aligned into 5 mu m wide patterns of another biomolecule is demonstrated through fluorescence imaging and atomic force microscopy. (C) 2008 American Institute of Physics.