Scan Options
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The Scan Options allows you to define Filters and Exclusions to discard when comparing two folders.
You'll see a "tree" options on the left:

Exclude Filters.
On the right (settings window), is a "main switch". You can define your filters anyway (Exclude Filters), but need to check this option to enable filters permanently (you may change this setting anytime). You have alternatives on Options menu to change Filters and Exclusions settings temporary for your current Comparator Fast
's session.

Other Scan Options.