Windows wakes up my external hard-drive whenever a software opens directory tree
Solution 1:
One way to do it is to mount each drive as a folder on your C drive. Your C drive will still spin up, but I believe you were more concerned with the external drives in your question.
Here's an article with instructions on how to set it up: http://wiki.flexraid.com/2011/09/29/tips-mounting-your-drives-as-folders-on-windows/
Solution 2:
Usually this happens because the software has to scan the drives for data, even if there isn't any. Probably the best/only thing you can do is to unplug it if you have a certain reason or if it's bothering you.