Atomic force anodisation lithography has been used to create patterned silicon oxide nanostructures on a p-type silicon (100) substrate. Modification of these oxide nanostructures either by acid treatment or self assembly of 3-aminopropyltriethoxysilane yields a chemically heterogeneous surface containing hydrophilic and hydrophobic regions allowing the site-selective deposition of thin films of conductive polyaniline. Carbon nanotubes, with high carboxylic acid functionality, were immobilised on the patterned hydrophilic regions using condensation reactions. Due to the hydrophobic nature of the nanotube sidewalls polyaniline is found to adsorb to the carbon nanotube structure and has allowed the creation of patterned carbon nanotube–polyaniline composites. Such composite materials may prove to be useful in the field of molecular electronics. These two approaches allow the construction of what are basically positive and negative resists using polymers.