How to stop Windows auto creating root level folders??

I have a partitioned hard drive and I use the C drive only for systems and programs etc. All my personal stuff is kept on my E drive which I keep neatly organised with a folder structure that works for me. However Windows keeps automatically cluttering up my E drive by creating 10 root level folders, and even if I delete them they are recreated. I cannot understand why this feature exists, but more importantly how can I stop it from happening?? It makes it so confusing because I already have subfolders in my own folder structure with the same name and it's just confusing and a cluttered mess. I'd be so grateful if anyone can tell me how to stop this really annoying feature of window please...??

First of all, What are the names of these folders ? and certainly it is not a Windows feature. The Folders that are created by Windows on root level are $RECYCLE.BIN (contains deleted files), System Volume Information (contains System Restore points) among with other hidden files such pagefile.sys, hiberfil.sys under C: drive, they are hidden and you can not move to a sub folder. If you have folders created under E: drive then it must have been from some third party applications which you have to find out what it is and usually there's an option to configure where the folders should be created.

Firstly thanks for taking the time to reply, much appreciated! The folders created are as follows:

Application
Downloads
EBook
Music
Photo
PIMS
Podcast
Ringtone
StoryAlbum
Video

Given what you said and the names of the folders, I'm thinking it must be Samsung Kies 3 creating these folders. The default folder under the preferences in Kies is set a few subfolders deep so I don't understand why this is happening?? A quick google check and I can't see anyone else mentioning this issue either. I guess I could contact Samsung and ask them if it's Kies and if so how to stop it. (It was SO much better when you could just plug your phone in and use Explorer to view/edit/delete files instead of having to used specific software.)

Looking at these folders, I can assure that they are coming from some third party software that you've installed. Just go thru the applications and look at either the Options or Preferences which you can set it to save file(s) in certain folder of your choice.

Hope this helps !!!

EDIT: With Samsung smart phone, you can plug in the phone via USB and Windows should recognize it under "This PC" as another hard drive and you can open it with File Explorer. For example, Pictures you've taken will be in DCIM folder.

I'm sure it's got to be Kies because that's the only software I have likely to create a Ringtones folder. However as mentioned in my last post, my default folder that I set in the Kies Preferences is several subfolders deep which doesn't make sense then for it to be creating folders at root level. But I have nothing else installed other than bluestacks, browsers and text editors and I'm pretty sure it's none of those.

PS: with my Samsung Galaxy S5 when I plug it in I can see it in Explorer but when I click on it, Explorer says that the folder is empty, which of course it isn't. The only way to view the folders and files is via Kies. It was the same with the Galaxy S2 I used to have and I know iPhones are the same.