<p>Recent trends in materials science have exploited noncovalent monolayer chemistries to modulate the physical properties of 2D materials, while minimally disrupting their intrinsic properties (such as conductivity and tensile strength). Highly ordered monolayers with pattern resolutions <10 nm over large scales are frequently necessary for device applications such as energy conversion or nanoscale electronics. Scanning probe microscopy is commonly employed to assess molecular ordering and orientation over nanoscopic areas of flat substrates such as highly oriented pyrolytic graphite, but routine preparation of high-quality substrates for device and other applications would require analyzing much larger areas of topographically rougher substrates such as graphene. In this work, we combine scanning electron microscopy with polarization modulated IR reflection adsorption spectroscopy to quantify the order of lying down monolayers of diynoic acids on few layer graphene and graphite substrates across areas of ~1 cm². We then utilize these highly ordered molecular films for templating assembly of di-peptide semiconductor precursors at the nanoscale, for applications in organic optoelectronic device fabrication.<br></p><p></p>