An automated process for microcontact printing is provided, comprising the steps of providing a substrate and a stamp; automatically aligning the substrate and stamp so that the stamp is aligned relative to the substrate to impart a pattern to the substrate at a desired location and with a desired orientation on the substrate; applying an ink to the stamp, the ink including a molecular species adapted to form a self-assembling monolayer (SAM) on the substrate; contacting the stamp and the substrate; and separating the stamp from the substrate.