A self-assembled Cu(II)-based nanocapsule enables efficient and straightforward isolation of Sc3N@C80 from arc-processed raw soot. The newly designed Cu(II)-based supramolecular nanocapsule 5·(OTf)8 was used to effectively entrap fullerenes and endohedral metallofullerenes (EMFs) with different affinities depending on their size and shape. Moreover, we took advantage of the sharply different entrapment abilities of the 5·(OTf)8 cage