Filled carbon nanotubes are of interest for a wide variety of applications ranging from sensors to magnetoelectronic devices and going through the development of smart contrast and therapeutic agents in the biomedical field. In general, regardless of the method employed, bulk filling of carbon nanotubes results in the presence of a large amount of external nonencapsulated material. Therefore, further processing is needed to achieve a sample in which the selected payload is present only in the inner cavities of the nanotubes. Here, we report on a straightforward approach that allows the removal of nonencapsulated compounds in a time efficient and environmentally friendly manner, using water as a "green" solvent, while minimizing the residual waste. The results presented herein pave the way toward the production of large amounts of high-quality closed-ended filled nanotubes, also referred to as carbon nanocapsules, readily utilizable in the foreseen applications