The scanning tunneling microscope (STM) was used to modify wires of the high temperature superconductorYBa2Cu3O7−δ(YBCO) which had been fabricated by electron beam lithography in order to simulate realistic conditions of a fabrication process. The linewidth of the structures generated with the STM was well below 50 nm. For a deeper understanding of the mechanism responsible for the STM-induced modifications, the experiments were performed under ambient conditions, in ultrahigh vacuum, carbon dioxide atmosphere, and nitrogen atmosphere. Results indicate that both water and carbon dioxide are essential for the modification process on the YBCO wires. This suggests that the modification mechanism is based on a water-mediated electrochemical decomposition of YBCO in the field of the STM tip.