Nanoscale fabrication of silicon substrate in an aqueous solution based on the use of atomic force microscopy was demonstrated. A specially designed cantilever with a diamond tip, allowing the formation of a mask layer on the silicon substrate by a simple scratching process (Tribo-Nanolithography, TNL), has been applied instead of the conventional silicon cantilever for scanning. A slant nanostructure can be fabricated by a process in which a thin mask layer rapidly forms on the substrate at the diamond tip-sample junction along scanning path of the tip, and simultaneously, the area uncovered with the mask layer is etched. This study demonstrates how the TNL parameters can affect the formation of the mask layer and the shape of 3-D structure, hence introducing a new process of AFM-based nanolithography in aqueous solution.