Internal molecular scaffolding is created by the lateral association of molecules at specific vertical positions within a single molecular layer. In this paper, such internal scaffolding is demonstrated for both noncovalent and covalent interactions using diacetylene-containing precursors. Previously shown to form a covalent polymer backbone upon UV irradiation, diacetylenes are shown here to also exhibit noncovalent lateral interaction prior to polymerization. Preferential twist orientation of the methylene side chains and distinct methyl group orientation illustrate the presence of this noncovalent scaffolding. Upon formation of the cross-linked polymer backbone, alkyl chain crystallinity and end group orientation are not significantly altered, but the methylene chain twist orientation is decreased. Evaluated as a function of the vertical position of the scaffolding within the monolayer, all monolayers exhibit excellent long-range order as measured by the electron-transfer properties.