A method of chemically well-defined, scanning tunneling microscope-based lithography is presented in which one thiolate in a self-assembled monolayer is removed and replaced with a second thiol. This method is distinguishable from other lithographic replacement processes on SAMs in that a nonpolar solution and an uncoated tip can be employed. Elevated relative humidity was important in the facility of this process, suggesting an electrochemical mechanism for replacement. The resolution of features written with this process is ca. 10-15 nm. In nonpolar solution, the apparent heights of self-assembled decanethiolate and dodecanethiolate monolayers are reversed compared to those observed in images obtained in air. When the thiol solution was exchanged after the first replacement, writing with two different thiols was demonstrated.