Student or Learner
What's the difference between "clean" and "clean up"?
I agree with bhaisahab that more context would be helpful.
In general though, usually I hear "clean your desk" in the sense of removing dirt with a cloth and cleaning materials, whereas I tend to hear "clean up your desk" in the sense of organizing the objects on the desk (some people say "tidy up" for this sense, but that's not as common where I'm from).
"Clean your desk" could also be used and/or interpreted in the sense of organization, but at least where I'm from, "clean up" would refer pretty clearly to organizing and not the other way around.