Despite the continued scaling down of semiconductor manufacturing, traditional lithography‐based nanofabrication only produces thin film structures, not 3‐D shapes. 3‐D nanofabrication remains a major challenge, especially for semiconductor materials. Most 3‐D nanofabrication techniques, such as two‐photon printing and stereolithography, mostly work for polymer materials, not solid‐state semiconductor materials. Here, a method capable of fabricating sophisticated 3‐D nanostructures of silicon based on the subsurface swelling phenomenon using focused helium ion swelling is reported. Silicon nanosphere arrays, hierarchical nanospheres mimicking compound lenses, nano‐Taichi symbols, three‐layer nanotowers, and nanopumpkins have been demonstrated, which are challenging for existing nanofabrication technology. The produced silicon nanostructures exhibit super small surface roughness as small as 0.1 nm, two orders of magnitude better than existing 3‐D nanofabrication technologies normally above 10 nm. The super small surface roughness opens doors for many exciting applications in photonics, indicating small photon losses. Moreover, it is demonstrated ultraprecise fine‐tuning of critical dimensions of ready‐made nanostructures or nanodevices, such as tuning the tilting angle of the tip on the atomic force microscopy probe and reducing the nanogap between two metal electrodes from 200 to 4 nm, which is promising for improving nanodevice performances by tuning the critical dimensions to desired ranges.