The vibration of Fe3O4 nanoparticles in response to an alternating magnetic field can be sensitively detected using contact mode atomic force microscopy (AFM) combined with selective modulation of magnetic domains. While imaging patterned samples of magnetic nanoparticles with contact mode AFM, a magnetic field was applied to drive sample vibration. The field altered in polarity and strength according to parameters of an AC current applied to a solenoid located under the sample. The vibration of Fe3O4 nanoparticles was detected by a nonmagnetic AFM tip to map the changes in frequency and amplitude of the vibrating sample at the level of individual Fe3O4 nanoparticles and clusters. Colloidal lithography, was used to prepare patterns of Fe3O4 nanoparticles on a glass surface using the basic steps of mixing, drying and removing the surface template of latex spheres. Monodisperse latex spheres were used to guide the deposition of magnetic nanoparticles in the spaces between the close-packed spheres of the latex film. With a mixture approach of "two-particle" lithography, 2D arrays of patterned aggregates of metal nanoparticles were generated which formed a periodic, well-defined arrangement that was suitable for subsequent characterizations with magnetic sample modulation (MSM).