Hi again, READ THIS THROUGH AT LEAST ONCE TO MAKE SURE YOU ARE ON THE RIGHT TRACK AND IF THIS ISNT RIGHT FOR YOU DONT DO IT....
right I am assuming its a stock heatsink and fan on the card - look at pics in the link below to be sure its at least similar - and not an Arctic Silencer found on some retail cards etc.....by this I mean a smaller flatter heatsink / fan combo with a sticker on top saying the make or name etc with the fan being about 2" in diameter.
If so removing the card from the system carefully and placing it on a flat clean and dry surface (desk etc) with the fan facing down you should see several screws holding the heatsink and fan shroud and ramsinks on. The fan shroud will be 3 screws that look slightly different to the others and wont be metal screws but larger threaded plastic ones.
Use the link below to get an idea but ONLY take off the fan and shroud - you can see the 3 screws Im on about in the first pic in reverse - around the fan only.
http://www.tekbunker.com/forums/index.php?showtopic=1396
There are smaller screws for the metal plate with the pic on (very small screws - you can remove these ones and you would see the 2nd pic but its far quicker and easier to remove the fan AND shroud via the 3 screws from the back and you should be left with what you see in the 3rd pic. Notice in the 3rd pic that you can clearly see the 3 empty screw holes from around the fan shroud Im on about so you cant really get them wrong. Oh and you dont have to unplug the fan from the pcb as shown if you dont want to - you will have enough wire to remove and replace the shroud etc.
Then its a lot easier to clean out both the heatsink and fan assembly in one go with a DRY paint brush lightly or simply pick out fluff and blow on it. AGAIN BE DAMN CAREFUL and nothing should go wrong at all but be certain you are prepared and take it slow.
I hope you will find a literal dust clog which would be causing problems and from the pictures in that link you can see how easy it is for the thin fins on the heatsink to get clogged up pretty quickly. My own card gets clogged in about 3 months - and Im a neat and tidy person who doesnt smoke so its a pretty usual problem.