The selective removal of hydrogen from a passivated Si(100) surface with an ultrahigh vacuum scanning tunneling microscope (STM) allows nanometer-sized “templates” of clean Si(100) to be defined on an otherwise unreactive surface. Such depassivated areas have already been shown to react selectively withO2andNH3in preference to the surrounding H-terminated surface. This selectivity suggests two more sophisticated approaches to fabricating nanostructures with this technique: (1) selective metallization by thermal chemical vapor deposition, and (2) formation of ordered organic monolayers by reaction with specific organic molecules. In the first case, an intrinsic difference in the reaction rate of a metal precursor with the clean and H-terminated Si(100) surface results in selective deposition of a metal on the STM-patterned area. In order to prevent hydrogen desorption and loss of selectivity, the metal precursor must dissociate its ligands at relatively low temperatures. In the second case, the patterned surface is exposed to an organic molecule expected to react in a site specific manner with unsaturated Si dimer sites. An example of this site selective reaction is the[2+2]cycloaddition reaction between carbon–carbon double bonds and the Si dimer bond. Such reactions can result in the formation of spatially resolved nanometer-sized regions containing organic monolayers. In this article we describe progress toward the fabrication of nanostructures utilizing these two techniques. First, we discuss the use of a new amidoalane precursor for the selective chemical vapor deposition of aluminum on STM-patterned Si(100) surfaces, as well as the selective patterning of a nucleation promoter,TiCl4,commonly used to initiate aluminum film growth. We also discuss the selective chemisorption of norbornadiene (bicyclo[2.1.1] hepta-2,5-diene) on STM-patterned areas. STM images reveal the formation of a norbornadiene adlayer with indications of local ordering. Both of these methods show promise as techniques for the fabrication of nanostructures on Si(100) surfaces.