Please don't do that! That's not how these two different Program Files folders work.
In an x64 system, Windows creates two program folders: in Program Files are stored native, real 64-bit applications, Program Files (x86) stores the programs that aren't native 64-bit.
For instance most users use standard 32-bit web browsers. IE8 and Firefox have 64-bit versions available, but mostly because Flash player don't yet support 64-bit, when you download and install a browser it's by default 32-bit. In my x64 system, I've installed Lunascape, Firefox and Opera browsers, all are located in Program Files (x86) folder, none of them have a folder in Program Files.
Please excuse me, but I doubt you have exactly the same subfolders in both Program Files folders. That's not how it works. Check again, and you'll notice some programs are to be found in Program Files, some others in Program Files (x86). Only a few programs create folders on both locations. An example is MsOffice which can have a subfolder in both folders, but if you check the content of these two Microsoft Office folders, you'll notice they are different.
To uninstall programs and applications, use the programs own uninstall application, or rather an uninstaller as Control Panel > Programs and Features and Revo Uninstaller. Do not uninstall by deleting a program folder.