The structure of nanoclusters is complex to describe due to their noncrystallinity, even though bonding and packing constraints limit the local atomic arrangements to only a few types. A computational scheme is presented to extract coordination motifs from sample atomic configurations. The method is based on a clustering analysis of multipole moments for atoms in the first coodination shell. Its power to capture large-scale structural properties is demonstrated by scanning through the ground state of the Lennard-Jones and C$_{60}$ clusters collected at the Cambridge Cluster Database.