Three-dimensional (3D) nanostructures and nanodevices have attracted tremendous interest in the past few years due to their special mechanical and physical properties. Nanodevices using 3D nanostructures as the building blocks have been demonstrated to exhibit multifunctionality and functions that conventional planar devices cannot achieve. In this article, we report and review focused ion beam techniques for direct site-specific growth of 3D nanostructures and postgrowth shape modification of freestanding nanostructures by ion beam-induced chemical vapor deposition and ion-beam-irradiation-induced plastic bending, respectively. Such techniques have shown nanometer-scale resolution and accuracy in the fabrication of metallic nanoelectrodes, 3D pickup coils, nanogaps, and multibranched structures. Characterization of the resulting nanostructures shows that focused ion beam techniques allow conducting and superconducting freestanding 3D structures to be tailored in size, geometry, and integrated with planar electronic, mechanical, and superconducting nanodevices, potentially enabling lab-on-a-chip experiments.