Most focusing screens on pro bodies (e.g., F90x/N90s, F4, F5, F100) are removable. Take the focusing screen out* and use a microfiber cloth to clean it. (Tip: get the E-type screen for your camera. Not only does it provide useful alignment lines, you get a little tool that makes it easier to remove the focusing screen on your camera.)
But I suspect you don't mean "focusing screens." Instead, you mean that you see dirt and grime through the viewfinder and want to clean whatever is causing this. Dirt and dust can be on the mirror, focus screen, or prism, each of which is cleaned and maintained in a different fashion.
- Mirror — don't use compressed air, and don't use a cloth or fabric to clean the mirror. The mirror is very easily damaged by touch or force, and a damaged mirror can hinder autofocusing and metering. What I use to clean my mirrors is the Statbrush 2000, a small antistatic, camel-hair brush used primarily in darkrooms to get dust off negatives. For most users, mirror cleaning should be left to a professional repair shop, though.
- Focusing Screen — if it's removable, take it out and brush it off*. Don't use pressure or force, especially on the newer screens that show the autofocus sensor in use. Don't use liquids, either, as short of distilled water, bad-for-camera minerals or chemicals are present in virtually every liquid I've seen used to clean cameras, including bottled water. And most of the newer screens are multi-layer, so it's possible to get liquid in between layers, where it not only is visible, but almost impossible to remove.
- Prism — toughest to clean, and easiest to mess up. If your prism is dirty, have a professional clean it (especially true of the sealed F5 prism). If you're going somewhere where dust is a problem (African safari, for example), keep the camera in a sealed plastic bag when you're not using it. (Actually, the technique I now use is to put my entire camera case in a sealed plastic bag between shooting sessions.) If you don't, you'll be having a professional cleaning done every trip!
*The focus screen is often "shimmed" by Nikon to get it into proper alignment. Thus, as you take it out, the shims will come out, too. You need to note where the shims are and put them back in place when you reinstall the focus screen if you want the focus screen to be properly aligned.
