Controlling the solid-state polymerization of organic molecules to form crystalline materials remains a challenge for the synthetic chemist. In an effort to control reaction pathways through topochemistry, we have compressed the 1:1 naphthalene-octafluoronaphthalene cocrystal, C10H8 center dot C10F8. This starting material displays a unique structure wherein the molecules are aligned in a nearly sandwich-like pi-pi stacking arrangement because of the inverse polarities of naphthalene and its perfluoronated derivative. This stacking arrangement and the use of fluorine as an sp(3)-templating functional group creates favorable interactions between the molecules along the crystallographic a axis, providing topological control over the reaction pathway at high pressure. Reaction of C10H8 center dot C10F8 along the molecular stacking axis to form polymerized sp(3) rods with single-crystalline order was confirmed through in situ single-crystal X-ray diffraction and infrared spectroscopy, as well as GC-MS analysis of the recovered polymerized material, and supported by computational models. Polymerization occurs at room temperature under rapid compression without uniaxial stress indicating enhanced control through the topology of the molecular precursor.