There are not many tools available (to be honest not a single one in my knowledge) to handle the privacy for "Files & Folders" (Zeitgeist) in Unity. However, an app is being rapidly developed and hope it would be included in 11.10.
At the time of writing, there is not much we do to it. Neither blacklist some folders, neither tweak the index settings. Even we can't delete any history items by using the GUI.
As a workaround, you need to manually delete some index files. Open up your /home directory in 'Nautilus' and press Ctrl + H to see the hidden files. Navigate to .local > share > zeitgeist and delete the file named 'activity.sqlite'. Now logout and back in or just restart the zeitgeist-daemon by entering this command in your Terminal: