Nanoscale science and technology is today mainly focused on the fabrication of nanodevices. Our approach makes use of lithography processes to build the desired nanostructures directly. The fabrication process involves an electron-beam lithography technique to define metallic microstructures onto which nanometre scale patterning is performed using an atomic force microscope (AFM) as a mechanical modification tool. Both direct material removal and AFM-assisted mask patterning are applied in order to achieve the smallest possible separation between electrode pairs. The sample preparation involves a polymer deposition process that results in conformal growth and in surface roughness comparable to that of the substrate. The results of the application of this technique show that the process is reproducible and exhibits a good operation control during the lithographic steps, both ensured by the imaging facilities of the AFM. The nanolithography technique has been used to fabricate nanogap electrodes to be used for molecular devices. The study reported here can be considered as a reliable starting point for the development of more complex nanodevices, such as single-electron transistors.