This paper reports a novel lithography method that utilizes local nanoscale thermal decomposition of polycarbonate films using heated atomic force microscope cantilever probe tips. The effect of polycarbonate structure and physiochemical properties on the lithographic performance of the thermal writing process have been explored. It is observed that amorphous linear polycarbonates which possess glass transition temperatures lower than their decomposition temperature generally exhibit substantial thermal deformation during thermal writing. In contrast, thermal writing on crystalline regions of semi-crystalline linear polycarbonate films produced good pattern definition. However, the semi-crystalline nature of the film results in substantial surface topography in the thin film which is undesirable for high resolution patterning and the amorphous regions of the film still suffer from local thermal deformation during writing. Amorphous cross-linkable polycarbonate sacrificial polymers have been synthesized and are shown to be able to resist thermal deformation of features during writing and are shown capable of producing good patterned images using the heated AFM probe writing technique.