The crystallization of amorphous germanium telluride (GeTe) thin films is controlled with nanoscale resolution using the heat from a thermal AFM probe. The dramatic differences between the amorphous and crystalline GeTe phases yield embedded nanoscale features with strong topographic, electronic, and optical contrast. The flexibility of scanning probe lithography enables the width and depth of the features, as well as the extent of their crystallization, to be controlled by varying probe temperature and write speed. Together, these technologies suggest a new approach to nanoelectronic and opto-electronic device fabrication.