Nanoscale DNA surfaces are manipulated by coating ultraflat gold with short thiolated single-stranded (ss) and double-stranded (ds) DNA. Hybridization and 6-mercapto-1-hexanol (MCH) are used to modulate the thickness of the layers, all the changes being monitored using atomic force microscopy (AFM) in situ. Short thiolated ssDNA forms irregular 3.5 nm thick coatings, which are converted into more uniform 6.0 nm thick layers upon hybridization with complementary DNA. Holes formed in a monolayer of short thiolated dsDNA can be partially filled with a longer length thiolated ssDNA, which then protrudes from the surface after hybridization with a complementary strand. MCH is used to modulate the depth of a ssDNA layer and improve hybridization to it.