The controllable deformation of nanopores was realized by moving a convergent electron beam in a high-resolution transmission electron microscope. Nanostructures with the desired geometries were successfully fabricated from the original nanopores in 100 nm-thick and 260 nm-thick Si(3)N(4) membranes. The formation dynamics is a competition process between the knock-on effect of the high-energy electron beam and surface tension driven shrinkage. This approach can be used to finely tune critical dimensions and deform nanopores to particular desired geometries with single-nanometer precision, which offers substantial opportunities in flexibly fabricating nanostructures for various applications such as nanoelectronics and nanofluidics.