Apparently the FN key is not handled by the Windows keyboard driver, but rather by drivers developed by Lenovo. Hence remapping of the FN key is impossible by any Windows utility that switches keys, because the Fn key doesn't generate any scan-codes.
Apparently Lenovo is currently considering a modification to the BIOS that will make this possible. See this article: "Switch Mode for Fn/Ctrl Keys".
In conclusion you should (1) regard your BIOS to see if such an option already exists, and if not (2) check the Lenovo site for BIOS upgrades from time to time (just note that BIOS upgrades need to be done very very carefully, since a mistake means bricking your computer).
In the meantime, you can use this solution (just joking):
I've tried using the Boot Camp drivers, but it was in the Mac .dmg format and I couldn't open the package. When I finally got around to opening it, all I could do was install the entire Boot Camp package -- which I didn't want to do considering it might overwrite drivers and make a royal mess. All I wanted was keyboard and the only thing I ended up with was a 32-bit package (couldn't find the 64-bit keyboard package) so I ended up using RandyRants' SharpKeys and AutoHotkey. I use them both anyway.
I have an Apple Pro Keyboard (graphite) and use it in Windows Vista -- I use Randyrants.com's SharpKeys to map:
F13 -> PrintScreen
F14 -> Scroll Lock
Left Alt -> Left Windows
Left Win -> Left Alt
Right Alt -> Right Windows
Right Win -> Left Alt
(since the Win key belongs between Alt and Ctrl)
The only thing SharpKeys can't do is Pause-Break, which appears to use a three-byte scancode which native Windows key-remapping can't handle (it'll just fire NumLock instead)
For Pause-Break, I added a definition to my AutoHotkey ahk file:
F15::
Send {Break}
return
The Eject key still doesn't work -- this seems to be a special key handled differently, as Eject can be used before an OS is even running.
ymmv, especially on newer Apple keyboards. As long as it produces a scancode, SharpKeys should be able to do it. The only troublesome key is Pause-Break.
SharpKeys is here : http://www.randyrants.com/2008/12/sharpkeys_30.html
Best Answer
Lenovo laptops (2008 models and newer) have a setting in the BIOS to switch these two keys.
There is no other way to do it except in the BIOS, because the Fn key is intercepted in hardware (only in combination with other keys), and never shows up in the operating system.
If you are not using the keyboard with a Lenovo branded system, you may not be able to do it at all.