This work represents our initial effort towards the fabrication of complex nanopatterns with automated scanning probe lithography (SPL). A multi-mode scanning probe microscope is linked with a computer-controlled vector-scan module to allow precise, automated control of the tip motion. The module is interfaced with computer-assisted design (CAD) and VLSI software, and programming capabilities are developed. We also provide a pathway for integration of our apparatus with external instruments. The capability to rapidly produce complicated nanopatterns is demonstrated using AFM fabrication of thiol self-assembled monolayers.