A set of structures can be classified by their maximum common substructures (MCS). Structures sharing the same MCS belong to the same group (or cluster). First level clusters can be grouped further based on their MCSs. Such hierarchy allows easy navigation through a set of structures, and also helps the assessment of its diversity. Typically a focused set of 1000-10000 structures obtained by virtual screening is analysed this way. The maximum common structures correspond to the scaffolds found in the set.