Yes, SearchBlox's collection filters let you add disallow paths under Collections > Paths > Disallow Paths.
For example, /cgi-bin/ would be a pattern to disallow the collection from having any documents which have /cgi-bin/ in the URL/directory path. The Disallow Path uses regular expressions, but you can create complex patterns by understanding the regular expression engine.
To learn more on HTTP Collection settings read: HTTP Collection Settings in SearchBlox
To learn more on File Collection settings read: File Collection Settings in SearchBlox