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The transporting colloidal particles, large molecules, cells, and other materials across surfaces and for assembling them into highly regular patterns are introduced through a method, where nonmagnetic materials are manipulated by a fluid dispersion of magnetic nanoparticles. Manipulation of materials is guided by a program of magnetic information stored in a substrate. Dynamic control over the motion of nonmagnetic particles can be achieved by reprogramming the substrate magnetization on the fly. We have developed methods for magnetically manipulating materials in a programmable fashion without requiring their attachment to magnetic particle carriers, which is the most common magnetic manipulation scheme. This developed manipulation techniques are not a stand-alone process, and they must be assisted by surface forces, based on molecular recognition, morphological templating, and/or photo-initiated chemical reactions.