A new platform of highly sensitive chemical and biological sensors using microcantilever arrays as transducers has emerged. In the critical step of functionalization, a chemically selective layer is deposited onto the cantilever surface making the sensor specific to binding or adsorption of a target analyte. Very precise deposition in volume and spatial accuracy has been achieved through the development of an inkjet functionalization system. In this paper, the methods for achieving maximum resolution are discussed. A high precision motion control system is presented which includes an X-Y stage powered by linear electric motors to achieve sub-micron positioning. A novel laser-optical registration method is developed to achieve the desired accuracy between the nozzle tip and the substrate. The inkjet functionalization system has enabled research to understand the effects of polymeric coatings on cantilever stiffness and quality factor. The system has been used to functionalize microcantilevers with magnetic micro beads using biotin-streptavidin binding.