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In this paper, we describe a novel method of fabricating polymeric 3-D magnetically driven microtools (MMTs) for performing nonintrusive and contamination-free experiments on chips. In order to obtain precise and complicated 3-D patterns from magnetically driven 3-D microtools, a grayscale photolithography technique was applied by making good use of a thick negative photoresist as a sacrifice mold. By controlling the amount of ultraviolet light with a gradation of gray-tone mask, we fabricated a smoothly curved (100-?? m gap) object without steps, which tend to appear in the case of conventional layer-by-layer photolithography techniques. A wide range of on-chip applications of microactuators can be realized by using the softness of the polymer-based 3-D MMT. For example, a microfilter and a microloader were successfully operated by a combination of magnetic and fluidic forces. The finite element method analysis of flow showed that a rotation of the 3-D MMT produces a relatively strong downward axial flow, which prevents particles from stagnating on the surface of the MMT. The produced 3-D MMT can be applied to complex on-chip manipulations of sensitive materials such as cells.