If you sand it down, be sure you don't sand too deep of you'll sand the veneer clean off. raw MDF is highly unattractive. If the scratches are deeper than the veneer, the cheapest option (not the best, but it will lessen the eyesore) is to buy some cherry wood putty or even a touch-up stick from a moulding shop. Or perhaps Lowes/Home Depot carries the stuff. If the surface was solid cherry, you wouldn't have to worry about sanding too deep. Or, depending on the desk... you might even just replace the entire desktop.