See the best way to protect these subfolders is to chmod them to +750 - that way no one from the outside world can get to those directories - but your own files in the main directory can call them and read off them...
A good way of stopping bots from indexing these is to play around with the settings in robots.txt file OR
I'd suggest an alternative method - I find very useful. Create a completely blank index.html file with just <HTML></HTML> tags and place it in these directories. When the bots - or any random surfer gets to your directory by guesswork - they're forced to a dead halt right there with a completely blank page... Otherwise, say, if your directory contains only images, anyone can view all your images in a directory listing format by entering the whole URL+directory in the browser.. but having a blank index.html stops that completely. That way you don't even need to mess around with chmod. Simple but Very Effective

Regards,
m^e
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