Microstructured optical fibers form a new class of extreme aspect ratio templates that are well-suited for precise, designed spatial organization of materials and molecules at dimensions down to the nanoscale. The extreme aspect ratios of the nanoscale to microscale pores in the templates necessitates new approaches to fabrication of nanowires, nanotubes, and self-assembled monolayers within them. High-pressure fluids, which have lower viscosities than liquids and no surface tension, are well-suited for penetrating such extreme aspect ratio capillaries. Here we report an approach to fabricating self-assembled monolayers within microstructured optical fibers using near supercritical or supercritical carbon dioxide. An AFM-based "shaving" technique has been developed to characterize the monolayers formed in capillaries that are too small to allow for characterization by conventional approaches.