Self-assembled monolayers (SAMs) covered with nitroso end groups were reduced using an atomic force microscope. As the bias voltage become more negative (beyond -4 V), the surface potential of the scanned area become closer to that of the amino-terminated SAM. Following this chemical change, however, no change in topographic features was detected, implying retained stability of the underlying SAM layer. We then released carboxylate-modified polystyrene (PS) spheres into a pH 4 solution containing the sample. Subsequent imaging with atomic force microscopy (AFM) revealed that these PS spheres were only selectively immobilized on the regions that were originally scanned at -6 V to form amino termination. In summary, using AFM set to a specific voltage, we were able to selectively generate micropatterned regions of the SAM with amino termination.