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New types of functional material structures will emerge if the shape and properties are controlled in three-dimensional nanodevices. Possible applications of these would be nanoelectronics and medical systems. Magnetic nanoparticles (MNPs) are especially important in electronics such as magnetic storage, sensors, and spintronics. Also, in those that are used as magnetic resonance imaging contrasts, and tissue specific therapeutic agents, as well as in the labeling and sorting of cells, drug delivery, separation of biochemical products, and in other medical applications. Most of these applications require MNPs to be chemically stable, uniform in size, and controllable in terms of their magnetic properties and shape. In this paper three new functions of iron (Fe)-based nanoparticles are reported: shape transformation, oxidation prevention, and self-alignment. The shape of the Fe nanoparticles could be controlled by changing their oxidation states and properties by using a nanocarbon coating. Full field X-ray microscopy using synchrotron radiation revealed controllable magnetic properties of MNPs at the L 3 edge which depended on the oxidation states. Then, inkjet printing was successfully performed to deposit a uniform layer of MNPs by the size.