Methods and systems for sorting nanostructures, such as nanodot or nanotubes, are described. The sorting of the nanostructures removes remnants of the nanotube fabrication from the mixture or bundle of material. The sorting includes suspending the mixture in a plasma, which separated the nanostructures and remnant material. A motive force, such as gas flow or laser, is applied to the suspended nanostructures and remnants such that the larger material moves out of the plasma while the smaller material remains trapped in the plasma.