A monolayer of hexadecyltrichlorosilane, 3-aminopropyltriethoxysilane or 3-mercaptopropyltrimethoxysilane was self-assembled onto a p-type silicon (100) substrate to provide a resist for electrochemical anodization with an atomic force microscope cantilever. Silane treatment of the oxide nanostructures created by anodization lithography allowed for the creation of a chemically heterogeneous surface, containing regions of -NH(2) or -SH surrounded by -CH(3) functionality. These patterned regions of -NH(2) or -SH provided the point of attachment for citrate-stabilized gold colloid nanoparticles, which act as 'seed' particles for the electro-less deposition of gold. This has allowed the creation of gold wires on a silicon surface. Carbon nanotubes, with high carboxylic acid functionality, were vertically immobilized on the patterned gold wires with the use of a cysteamine monolayer and a condensation reaction. Such a material may prove useful in the creation of future vertically integrated electronic devices where it is desirable for electron transport to be in three dimensions and this electron transport is demonstrated with cyclic voltammetry.