A novel stitching method is presented which does not require special purpose alignment markers and which is particularly adapted to probe lithographic methods, enabling the writing of large patterns exceeding the size limitations imposed by high precision scan stages. The technique exploits the natural roughness of polymeric resist surfaces as a fingerprint marker for the sample position. Theoretical and experimental evidence is provided that sub-nanometer metrological accuracy can be achieved by inspecting the surface roughness in areas with 1μm linear dimensions. The method has been put to the test in a thermal probe lithography experiment by writing a composite pattern consisting of five 10μm ×10μm fields which are seamlessly joined together. The observed stitching error of 10nm between fields is dominated by inaccuracies of the scanning hardware used in the experiment and is not fundamentally limited by the method perse. © 2012 IOP Publishing Ltd.