This paper provides a convenient method for fabricating highly controlled arrays of gold nanoparticles on silicon by combining AFM nanolithography and self-assembly techniques. Our main methodology is to fabricate nanopatterns on silicon, covered with amino group and methyl group terminated self-assembled monolayers (SAMs), at different surface locations. These nanopatterns were then used to guide the assembly of gold nanoparticles according to their different affinities for amino and methyl groups. AFM was employed to induce a localized degradation of the methyl SAM on the silicon and therefore to control the amino SAM-covering area for nanoparticle adsorption, where the amino SAM was formed on the degraded regions by the conventional self-assembly technique. Gold nanoparticles (15 nm in diameter) selectively assembled at the AFM tip-defined amino regions, forming precisely positioned nanoparticle arrays. Such kinds of highly ordered nanoparticle assemblies are believed to contribute to the studies of nanoelectronic devices and mesoscopic phenomena.