Nanoscale control of surface chemistry holds promise for tailoring the electronic, optical, and chemical properties of graphene. Toward this end, the nanofabrication of sub-5-nm heteromolecular organic nanostructures is demonstrated on epitaxial graphene using room temperature ultrahigh vacuum scanning tunneling microscopy. In particular, monolayers of the organic semiconductor 3,4,9,10-perylene-tetracarboxylic dianhydride (PTCDA) are nanopatterned on epitaxial graphene using feedback-controlled lithography (FCL) and then used as chemical resists to template the deposition of N,N'-dioctyl-3,4,9,10-perylene-tetracarboxylic diimide (PTCDI-C8). The generality of this FCL-based nanofabrication procedure suggests its applicability to a wide range of fundamental studies and prototype device fabrication on chemically functionalized graphene.