Cleaning a server is always a bit tricky, especially when you CAN'T turn it off.
Fortunatly the fans on the cpu coolers come off and move out the way fairly easliy in my particular setup so managed to get the dust off them nicely! Another small job done and dusted. ;)
do you use one of those canned air mcjiggers?
No, I just use my hoover with brush nozzle attachment and very gently coax the dust off so it's clean enough. Normally I have a small paint brush I use to brush the dust off the heatsinks but I donno where it is atm xD
Those brush attachments do not get nearly enough attention in the world of electronics repair!