When you create the output XML files, System Architect dumps all encyclopedia records into those files. The Compare Filter sets enable you to select which encyclopedia records to compare. Compare Filter sets are displayed in a drop-down list on the Input tab. The Compare Filter dialog displays all the records found in output file, and you check or uncheck the diagrams and definitions to compare. You can add and remove your own Filter sets, but you cannot remove the Default Filter set.
A benefit of using Compare Filter sets is that from the same pair of output files, you can run different comparisons, where each run compares different data.