A Multiple Structural Alignment algorithm is presented. The algorithm accepts an ensemble of protein structures and finds the largest substructure (core) of C atoms whose geometric configuration appear in all the molecules of the ensemble (core). Both the detection of this core and the resulting structural alignment are done simultaneously. Other large enough multi-structural superimpositions are detected as well. Our method is based on the Geometric Hashing paradigm and a superimposition clustering technique which represents superimpositions by sets of matching atoms. The algorithm proved to be efficient on real data in a series of experiments. The same method can be applied to any ensemble of molecules (not necessarily proteins) since our basic technique is sequence order independent.