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Electron-transparent substrate that can specifically capture tagged protein complexes prompted us to fabricate a template that allow capture and structural studies of biotinylated protein complexes by transmission electron microscopy (TEM) to understand protein-protein interactions. Here we present a novel method that allows the scalable extraction and individualization of the tiny fraction of small diameter SWNTs that is functionalized with neutravidin, which can be used to bind biotinylated species. Atom force microscopy analysis indicates 98% purity of the individualized small diameter SWNTs (diameter range: 0.4-0.7 nm, length range: 100-1000 nm). The method includes two steps of functionalization-centrifugation based on the size selective properties of neutravidin toward the SWNTs and results in a sparsely neutravidin-functionalized population: about 1 biotin-specific neutravidin complex per 1000 nm of SNWT. The new method can be scaled up to mass production. This widely opens the door to the bulk characterization of its special (electronic) properties and will allow new, unprecedented applications of this fascinating material, such as electronic devices and novel biochemical applications. The SWNT-neutravidin could be used as a scaffold to analyze protein structure directly by cryo-transmission electron microscopy, which provides better understanding in protein-protein interactions and biological processes.