A system and method for manipulation of nanotubes using an organic material that is presented to the nanotubes. Exemplary types of manipulation include cutting nanotubes into shortened nanotubes, dispersing nanotubes, enabling dissolution of nanotubes, and noncovalently functionalizing nanotubes. The organic material used in manipulating nanotubes preferably comprises a solid organic material, soluble organic material, and/or an organic material that acts as a dispersing reagent for dispersing nanotubes. In a preferred embodiment, the organic material used for manipulating nanotubes comprises cyclodextrin.