The biofunctionalization of nanoelectromechanical systems (NEMS) is critical for the development of new classes of biosensors displaying improved performance and higher levels of integration. In this paper we propose a modified microcontact process (μCP) in order to biofunctionalize arrays of NEMS with a probe molecule on the active sensing areas together with an anti-fouling layer on the passive areas in a single, self-aligned step. We demonstrate the adequate functionalization/anti-fouling of arrays of freestanding nanocantilevers as dense as 105 nanostructures cm−2 by using both fluorescence microscopy and dynamic measurements of the structures' resonant frequency. The proper bioactivity of an antibody deposited onto the cantilevers and the blocking property of a bovine serum albumin layer are both assessed by incubating specific and non-specific tagged secondary antibodies followed by fluorescence imaging. Furthermore, measurement of the resonant frequency of the nanocantilevers before and after functionalization and biological recognition demonstrate that using μCP for device functionalization does not damage the nanostructures and preserves the mechanical sensing capability of our NEMS.