In this paper we describe a novel fabrication method of three dimensional polymeric magnetically driven microtools (MMT) for non-intrusive and no contamination experiments on a chip. In order to obtain precise and complicated three dimensional patterns of magnetically driven 3D microtools, a grayscale photolithography technique has been applied by making good use of thick nega-photoresist as sacrificed mold. By controlling an amount of ultraviolet light with a gradation of gray tone mask, we have fabricated smoothly curved (100 μm gap) object without steps which tend to be appeared in case of conventional layer by layer photolithography techniques. A wide range of on-chip application of microactuators can be proposed by using a softness of polymer-based 3D MMT. For example, microrotor was operated as miromixer and micropump, also microloader was actuated by the magnetic and fluidic force. The surface of the 3D MMT was fabricated with a group of spiked pattern to reduce the contact area between PDMS (Poly dimethyl siloxane) microchannel and PDMS-based 3D MMT. The produced 3D MMT can be applied to complicated on-chip manipulations of sensitive materials such as cells.