Masked genomes/sequence refer to genomic sequence that has been scanned for some type of internal sequence and then has those sequences converted to "X". Usually, repeat sequences are identified and masked as these cause sequence comparison algorithms to spend a lot of time identifying and matching these sequences. It is recommend to use repeat masked genomes in CoGe when given an opportunity for a whole genome comparisons (e.g. in SynMap)
Masking sequences come in two general flavors
Hard mask: Masked sequence is converted to "X"
Soft mask: Masked sequence is converted to lower-case ATCG