Abstract: A method for assembling and integrating microstructures (pills) onto a substrate. A plurality of patterned recesses are formed on the substrates, the recesses having transverse cross-sections and openings of specific shapes. A hard magnetic layer is deposited at the bottom of each said recess. A guide is positioned over the substrate, the guide having patterned hole shapes matching the shapes of the openings to the patterned recesses with which the holes mate. A collection of the pills is placed atop the guide. The said collection includes members with cross-sections matching the shapes of the openings to the recesses, and each pill is coated at one end with a soft magnetic layer. A moving magnetic field is applied to the collection of pills to agitate the pills, and effect a magnetic attraction between the layers at the ends of the pills and the soft magnetic layer at the bottom of the recesses.