Microcontact printing ( CP) of extracellular matrix proteins is a fascinating approach to control cell positioning and outgrowth, which is essential in the development of applications ranging from cellular biosensors to tissue engineering. Microelectronic devices can be used to detect the activity from a large number of recording sites over the long term. However, signals from cells can only be recorded at small sensitive spots. In this paper, we present an innovative setup to perform aligned CP of extracellular matrix proteins on microelectronic devices in order to guide the growth of electrogenic cells specifically to these sensitive spots. Our system is based on the combination of a fine-placer with redesigned micro stamps having a rigid glass cylinder as backbone for attachment in the alignment tool. Alignment is performed moving the device with an optical table under microscopic control of the superimposed images from stamp and device surface. After successful alignment, the stamp is brought into contact with the device surface by means of a high-precision lever. With our setup, we were able to pattern up to 40 devices per hour. A lateral alignment accuracy of 2 m has been achieved. Aligned neuronal growth on patterned devices was demonstrated with dissociated hippocampal neurons.