If you have Vista or Windows7, AND you installed your game in the default directory, then you will never see the mod in the data folder.
The GECK is NOT part of the game so the OS sees it as a virus or trojan program trying to change FO3 game files. This is not allowed by the OS.
Solution? Pick "one" of these:
1. Install your game to your Root C: drive. Like C:\Games\Fallout3\ or another drive entirely if you have one.
2. Remove the security from your OS and then you can join the XP computer ranks and become a Zombie computer. *Not recommended.
3. In your \Fallout3\Data\ folder, look at the top right. There should be a button called 'Compatibility Files'. Click that to find your mod. You can then copy it from there to your Data folder.
4. Run the GECK in Administrator mode. Right-click on the icon and select, Run as Administrator.
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Now, if you want to install the Fallout3 game somewhere else per #1 above without loosing your current mods you have installed, you can do this:
1. Move your existing \Program Files\Fallout3\ to your C root drive in a new folder that you need to create called C:\Games\ It should look like this after the move: C:\Games\Fallout3\
2. Rename the folder you just moved in step 1 to C:\Games\Fallout003\
3. Uninstall the game. Check the option to keep your save game files. This will clear the registry and not remove any game folders because you moved them somewhere else.
3. Re-install the game to C:\Games\Fallout3\
4. After the reinstall is done, DELETE the just installed folder at C:\Games\Fallout3\
5. Rename the folder from step 2 above to C:\Games\Fallout3\
If done right, this will change the Registry to the new game folders location, plus keep everything you currently have in the protected folder location.
WARNING: If you are not computer saavy, then find someone who is to do the above for you. Or ask more questions.