If it is the fan, then you can stop the motor with FCU for awhile and see if the smell goes away or lessens; I do, however, suspect it is something else if the fan is operating normally. The only other thing I could think of is that either something got stuck in a hot part of the Thinkpad and is now burning, or there is an insulation component on the wiring that is roasting.
You could, if you wanted to, run the Thinkpad with the keyboard detached, but still connected, to see if there is any smoke coming from the interals that you can see.