Many materials properties are tailored by controlling the chemical reactivity of surfaces. Consequently, through chemically active nanopatterning, surfaces can be engineered with nanoscale spatial resolution. This paper describes three techniques that enable the chemical reactivity of silicon surfaces to be customized down to the single molecule limit using scanned probe microscopy (SPM). All three techniques use chemically inert hydrogen passivated silicon as a starting substrate. Injected electrons and/or electric field from a conductive SPM tip locally disrupt the passivation, thus allowing the surface chemistry to be modified. Using ultra-high vacuum scanning tunneling microscopy, feedback controlled lithography leads to electron stimulated desorption of hydrogen from Si(100)-2×1:H with atomic resolution. The resulting dangling bonds preferentially react with gas phase molecules, enabling pre-determined self-directed growth of styrene molecular wires. In ambient conditions, conductive atomic force microscopy (cAFM) is used to grow nanoscale hydrophilic domains on Si(111):H via anodic field induced oxidation (FIO). Due to the chemical contrast between the hydroxyl terminated oxide and the hydrophobic Si(111):H surface, octadecyltrichlorosilane selectively binds to FIO nanopatterns. The final nanolithographic scheme, called liquid phase nanolithography (LPN), employs cAFM on surfaces submerged in organic solvents. By encapsulating the tip-sample junction in a solvent with low water and oxygen solubility, anodic oxidation is suppressed, thus enabling direct molecular attachment to the silicon surface from the liquid phase. In this work, LPN has been used to nanopattern undecylenic acid methyl ester. Nanoscale variations in the frictional properties induced by LPN and FIO are directly measured with lateral force microscopy. Through readily available and well-established chemical protocols, this nanolithography toolkit enables arbitrary materials, including polymers and biological molecules, to be covalently bound to silicon with nanometer spatial resolution.