A fully controllable process for the fabrication of carbon nanotube assemblies is presented on the basis of a sequential electrochemical oxidation lithography process. This approach utilizes the local chemical conversion of a n-octadecyltrichlorosilane self-assembled monolayer into a template featuring polar acid groups. The capability to utilize such chemically active templates for the site-selective assembly of individual carbon nanotubes was demonstrated, and a hierarchical, sequential structuring routine to obtain crossed CNT configurations, formed by preselected carbon nanotubes, was implemented. The introduced process allows the reliable and well-controlled fabrication of tailor-made nanoscopic assemblies of nanomaterials toward their integration into complex device frameworks and could provide control over the electrical properties of the fabricated assemblies.