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Nanoscale manipulation is a basic ability needed to realize many of the nanotechnology applications. We demonstrate an ion bean molding technique to shape the configuration of nanostructures. As an example, the native curvature of a carbon nanotube in an atomic force microscope tip and its undesirable angle with respect to the surface are removed by this technique to render the nanotube straight. The straightened nanotube is effectively used in a semiconductor profilometry application. The ion beam molding technique is also shown to be effective in creating a desirable net shape of nanotubes. As mechanical deformation determines electrical and other properties of nanotubes, such manipulation may be of use in nanodevice fabrication.