Thermal Scanning Probe Lithography  (tSPL) utilises a heated AFM tip to locally evaporate a polymer layer. Using tSPL nanometer precise 3D profiles can be formed in this polymer layer . tSPL offers a resolution and linear scan speed that is competitive  with the current state of the art maskless technique, Gaussian electron beam lithography. A recently developed pattern transfer technique allows for the subsequent transfer of these patterns into the substrate . Pattern alignment or overlay is a key challenge both in device fabrication and the investigation of novel nanostructures. tSPL has a pair of unique capabilities for meeting this challenge. Firstly it can read topography with sub-nanometer sensitivity and secondly reading the surface does not lead to resist exposure. This removes the need for dedicated alignment marks which in turn removes difficulties associated with marker degradation and inconsistencies in the positioning hardware used for read and write. Here we describe our efforts to implement and assess a markerless overlay process. In particular we investigate the two sources of error in the overlay process. The first are errors arising in the determination of the position of the existing pattern. We demonstrate theoretically that for our tSPL patterning stack the detection error may be some 200 times smaller than the 1μm feature size present in patterns produced using optical lithography. The second source of error is in the writing of the overlay pattern. We outline the practical steps including feed forward scanner control, on-the-fly drift correction and 3D patterning required to achieve nanometer accuracy in the pattern placement. © 2014 IEEE.