The various surface types involved in the synthesis of DNA upon alcohol-terminated monolayers at Si(111) surfaces were probed using scanning tunneling microscopy (STM). Images of the initial hydrogen-terminated layer showed the typical step and terrace features which are retained after alkylation with 4,4'-dimethoxytrityl-1-undecenol. The method of deprotection for oligonucleotides synthesized at these monolayer films was shown to have a dramatic effect on the surface. After treatment with methylamine, rinsing with water caused considerable etching of the surface; however, this was avoided by the use of a dry ethyl acetate and ether wash. There is, little indication of DNA for surfaces covered with single stranded material as judged by STM imaging or tunneling spectroscopy experiments. However, after hybridization with the complementary strand, DNA-Si(111) substrates gave stable images that do not typically show the step and terrace features of the underlying alkyl monolayer. Instead wormlike features are seen that are interpreted as containing aligned DNA molecules lying nearly parallel to the surface.