You can exclude directory from search results by adding exclude rules in the Console. If you want to exclude a specific directory then select either the dir1 or dir 2 field and set it to 'Equals', and then enter the directory name that you wish to exclude from search results.
For example, if you have a site called www.acme.com with a section containing legacy publications you wish to exclude at www.acme.com/old, you would create an exclude rule where 'dir1' equals 'old-directory'. This will remove all content from the index found within 'old'. If the content instead lived in www.acme.com/publication/old then you would set the rule where 'dir2' equals 'old'.