FYI: CHMOD won't help here. CHMOD is something the server uses to control who can and cannot access files on the server itself -- i.e. which users on the server. Outside of the server, it has no effect whatsoever.
Options -Indexes only prevents the server from listing directories' contents. Files, for instance
wp-content/plugins/plugin-file.php (that's made up) will still be accessible, and if Google could access it before, it'll still be able to access it now.
Another thing you may want to look into is robots.txt. This tells search engines what you do and don't want to be included in their indexes.
More info: http://www.robotstxt.org/
Bear in mind that this is accessible to anyone. Check it out:
All the major search engines read this file and respect it.
I would recommend, for you, something like:
This tells all search engines to leave those directories alone.
Incidentally, I recommend these lines, too:
This stops your site being archived in the Wayback Machine project.