The Folder branch under Configuration - Ignore Options has the following options:
Ignore files/folder types
This control may be used to add a semi-colon delimited list of folders, files, and file extensions to be ignored in Folder Compare Mode. For example, a user may enter ‘CVS’ and any time the file or folder CVS is located in a folder it will be ignored when executing and displaying a folder compare. A user may even enter an absolute path to a file/folder to be ignored. An asterisk (*) can be used as a wild card. In order to ignore all files of a particular type the asterisk will be used with the file extension. For example, a user may enter the line ‘*.txt;*.php;*.asm’ and the file extensions .txt, .php, and .asm will be ignored when executing and displaying a folder compare.