Polymerizable amphiphiles can be assembled into lying-down phases on 2D materials such as graphite and graphene to create chemically orthogonal surface patterns at 5-10 nm scales, locally modulating functionality of the 2D basal plane. Functionalization can be carried out through Langmuir-Schaefer conversion, in which a subset of molecules is transferred out of a standing phase film on water onto the 2D substrate. Here, we leverage differences in molecular structure to spatially control transfer at both nanoscopic and microscopic scales. We compare transfer properties of five different single- and dual-chain amphiphiles, demonstrating that those with strong lateral interactions (e.g., hydrogen-bonding networks) exhibit the lowest transfer efficiencies. Since molecular structures also influence microscopic domain morphologies in Langmuir films, we show that it is possible to transfer such microscale patterns, taking advantage of variations in the local transfer rates based on the structural heterogeneity in Langmuir films. Nanoscale domain morphologies also vary in ways that are consistent with predicted relative transfer and diffusion rates. These results suggest strategies to tailor noncovalent functionalization of 2D substrates through controlled LS transfer.