Finally! A puzzle with some entertainment value !!!
Now, let me see here...
You have a lot of files. They all have the same file-name, but differnet data. And they are all in separte folders.
This is best answered by describing what I did.
I did the following to reproduce the issue
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On my desktop I made a new folder titled "New Folder". Inside that I made 2 more folders and in each of the folders I put in a text file. My final directory structure looked like this,
\Desktop\New Folder\New Folder\New Text Document.txt
\Desktop\New Folder\New Folder (2)\New Text Document.txt
\Desktop\New Folder\New Text Document.txt
Now what I need to do is figure out an easy way to rename all those text documents.
This is what I did to rename the files
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I opened up Start>Search
I did a search for *.txt file in \Desktop\New Folder
I got a list of 3 files all named "New Text Document.txt"
Now (this is the important part), I selected them all, right-clicked and renamed the top file to "File.txt".
The resulting directory structure I got looked like this,
\Desktop\New Folder\New Folder\File (1).txt
\Desktop\New Folder\New Folder (2)\File (2).txt
\Desktop\New Folder\File.txt
I think I achieved what was desired now. The files are renamed and your directory structure is maintained.
Give it a shot and tell us how things went !! ( You might want to conduct an experiment first, to confirm things yourself )
Oh, and I should have mentioned this earlier, I'm using XP. But this method should work with any Windows OS.