A challenge in nanofabrication is to overcome the limitations of various fabrication methods, including defects, line-edge roughness and the minimum size for the feature linewidth. Here we demonstrate a new approach that can remove fabrication defects and improve nanostructures post-fabrication. This method, which we call self-perfection by liquefaction, can significantly reduce the line-edge roughness and, by using a flat plate to guide the process, increase the sidewall slope, flatten the top surface and narrow the width while increasing the height. The technique involves selectively melting nanostructures for a short period of time (hundreds of nanoseconds) while applying a set of boundary conditions to guide the flow of the molten material into the desired geometry before solidification. Using this method we reduced the 3σ line-edge roughness of 70-nm-wide chromium grating lines from 8.4 nm to less than 1.5 nm, which is well below the ‘red-zone limit’ of 3 nm discussed in the International Technology Roadmap for Semiconductors. We also reduced the width of a silicon line from 285 nm to 175 nm, while increasing its height from 50 nm to 90 nm. Self-perfection by liquefaction can also be extended to other metals and semiconductors, dielectrics and large-area wafers.