What are you changing it to?  And what do you have in there right now?
If you are changing it to sand, or have sand in there right now, than yes, you will need to completely empty the tank.
But if you are changing it from gravel to a different type of gravel, you could probably get away with just scooping the gravel out, and then replacing it carefully with the new substrate.
However, I would still recommend taking everything out, that way you could also do a quick clean on the tank.
-FHM