Generally speaking I'd avoid using a vacuum cleaner to clean the inside of your computer. Vacuums potentially create enough static to wreak havoc on your components. Plus, you run the risk (albeit small) of it sucking something out of your computer you'd just as soon not lose.
An alternative would be a can of the compressed air. Then, have the vacuum a safe distance from the computer, collecting the dust the air can blows out of the case. Also, there's this thing on the front of your face, called a mouth, that is pretty good at blowing dust out of an opened case <g>.