First time posting, restoring files to proper folders/libraries

Hello:

Though the Windows 7 method of storing files/folders in libraries, I am encountering problems I never have seen in XP. My Documents file is so cluttered with files that do not belong there that I have created an XP like file storage system on my C: drive.

I do not know how, but the libraries in Windows 7, especially My Documents, contains script files, image files (not pictures but graphics that are part of search engine or browser window), to the point that searching for an actual document is useless. I have created a folder off the C; drive that has sub-folders & files stored in them that I deliberately store there so I can access them. This isn't healthy for the PC because I know that Windows 7 is also making a copies for My Documents within My libraries of the same file. It is an ad hoc procedure used because it took so long to wade through the extraneous files incorrectly stored in My Documents. (To a lesser extent the same problem is true with My Music, My Pictures etc). Since I don't know the types of many of the files mistakenly filed in My Libraries>My Documents, it would be impossible for me to go through each file and correctly assign it to its proper folder.

Is there a Windows utility, or an effective aftermarket utility, that is capable of going through all of the files on a PC and correctly assigning them to their home? Is there a system setting I should check that would ensure the files are correctly stored? I have gone through the file associations to ensure they were correct. I would greatly appreciate any help in this matter. Thanks.