This document summarizes improvements to ChemAxon's Maximum Common Substructure (MCS) search module. The new module has improved accuracy and run time, reduced memory usage, and reduced fragmentation compared to previous versions. Extensive tests show major improvements in these areas, including faster running times (e.g. from 20 minutes to 2.5 seconds on difficult structures), fewer fragments identified, and identification of more common bonds. Examples are provided to illustrate the improvements.