Somewhere on your computer lives the httpd.conf file, the main config file for apache. There's a section in it that says "This should be changed to whatever you set DocumentRoot to." Shortly after that comes a directory container something like:
<Directory "/www/htdocs">
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
Allow from all
</Directory>
If you remove the word "Indexes" from the Options line, and restart your web server, then you should no longer have indexes show up in directories under your document root, unless you create a new container for a subdirectory that turns auto-indexing back on.