A method for migrating a selected set of virtual machines from a first volume to a second volume. The method includes receiving a list of virtual machines which are not migrating from a first volume to a second volume, accessing a host file system usage map of a host machine that indicates active blocks of the host file system, and accessing virtual file system usage maps of a plurality of virtual machines that indicate active blocks. A filter usage map that identifies the active blocks of the virtual machines which are not migrating is generated. The plurality of virtual machines are migrated from the first volume to the second volume, wherein the active blocks of the virtual file systems which are not migrating are skipped in accordance with the filter usage map. Subsequently, the metadata at the second volume is processed to reflect the virtual machines which were not migrated.