Denying access to folders

New to permissions so I hope I can get some help!

By default the folders on my user/domain are set as open to be accessed by anyone. I simply want to make it so that directories cannot be accessed but the files within them can. How can I do this?

I often put a blank index.php file in all folders to avoid people browsing a dir listing.

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I put -Indexes in my .htaccess file.