A relatively fast, inexpensive, and non-destructive method for separation and isolation of biologically active nanoparticles is described. Methods include the use of solid phase separation medis such as channeled fibers in a hydrophobic interaction chromatography (HIC) protocol to isolate biologically active nanoparticles from other components of a mixture. Biologically active nanoparticles can include natural nanoparticles (e.g., exosomes, lysosomes, virus particles) as well as synthetic nanoparticles (liposomes, genetically modified virus particles, etc.)