I have some config files and private directories not to index by any search engine specially yahoo. that's why
Exclude them in your robots.txt. If they are not following your robots.txt directives, you can block from those directories using your .htaccess. Robots.txt is the recommended method. Also, turn off indexing in your .htaccess so it won't reveal files in each directory.
You might consider using secure servers, the ones needing log in for this purpose, or create several directories and block them from getting indexed from your homepage Robots file.