Thermally deposited monolayers of the DNA base guanine have been studi
ed by scanning tunneling microscopy (STM) and a novel scanning thermop
ower microscope (STPM). The STPM signal provides a distinct representa
tion of the monolayer lattice not present in the STM signal. The inten
sity of the thermopower contrast is dependent on the temperature gradi
ent at the tunnel junction. Surface roughness and topographical variat
ions of the underlying substrate are not convoluted with the signal du
e to the feed-forward acquisition method of this technique. A plausibl
e interpretation of the STPM signal and images is proposed, and the pr
ospects for single molecule differentiation and spectroscopy are discu
ssed.