Systematic studies on scanning probe lithography (SPL) methodologies have been performed using self-assembled monolayers (SAMs) on Au as examples. The key to achieving high spatial precision is to keep the tip-surface interactions strong and local. Approaches include three atomic force microscopy (AFM) based methods, nanoshaving, nanografting, and nanopen reader and writer (NPRW), which rely on the local force, and two scanning tunneling microscopy (STM) based techniques, field-induced desorption and electron-induced desorption, which use electric field and tunneling electrons, respectively, for nanofabrication. The principle of these procedures, the critical steps in controlling local tip-surface interactions, and nanofabrication media will be discussed. The advantages of SPL will be illustrated through various examples of production and modification of SAM nanopatterns.