Nanoparticle lithography takes advantage of the self-assembly of monodisperse particles into either 2D or 3D periodic structures for patterning materials. We have developed reproducible methods to fabricate arrays of nanostructures on flat surfaces using monodisperse latex spheres. In a solution-based "mixture" method for nanopatterning proteins, polystyrene latex are mixed in aqueous solutions with proteins and dropcast onto ultraflat substrates. The mixtures containing latex self-assemble into organized crystalline layers on surfaces when dried. Latex nanospheres are easily displaced from the surface by rinsing with water. However, proteins are not rinsed away and remain attached to the surface forming a monolayer of exquisitely arranged regular nanostructures which reflect the order and periodicity of the latex scaffold. We have also developed a second method for nanopatterning silane monolayers using vapor deposition. Aqueous solutions of latex nanospheres self-assemble into organized crystalline layers on flat surfaces when dried, to form a structural template or mask on mica(0001). The substrate is then placed in a sealed container containing organosilanes such as octadecyltrichlorosilane. A vapor is generated by heating at 60 C under ambient pressure. Silane SAMs deposit on the surface in the void spaces between spheres during vapor deposition. Latex particles are completely removed by rinsing the surfaces with ethanol and deionized water. Changing the length of the deposition intervals provides insight into the evolution of deposition processes on surfaces. Silane molecules with various terminal groups exhibit different adsorption phenomena when applied to templated surfaces as vapors. Methyl-terminated silanes display strong attraction to the latex particles to form meniscus ring-shapes near the latex spheres. Thiol-terminated silanes deposit in the interstitial areas and form cavities surrounding the particles. Topographic AFM images will be presented exhibiting the morphology and periodicity of nanostructures can be tuned by selecting various sizes of latex spheres and by changing experimental parameters.