Nanomaterials derive their electronic, magnetic, and optical properties from their specific nanostructure. In most cases, nanostructured materials and their properties are defined during the materials growth, and nanofabrication techniques, such as lithography, are employed subsequently for device fabrication. Herein, a perspective is presented on a different approach for creating nanomaterials and devices where, after growth, advanced nanofabrication techniques are used to directly nanostructure condensed matter systems, by inducing highly controlled, localized, and stable changes in the electronic, magnetic, or optical properties. Then, advantages, limitations, applications in materials science and technology are highlighted, and future perspectives are discussed.