If you are prototyping, why are you thinking about clean code? The very idea of prototyping is that it's meant to prove a concept or idea, and to be thrown away afterwards.
I'm going to disagree with most everyone here by saying that if you are already thinking about the choice between writing clean code or getting something done quickly for prototyping, choose the latter. Especially when you're talking about early stage development. I'm not saying don't ever write clean code, I'm saying get the idea out, see that it's the direction to go, then go back clean it up-- refactor.
As software developers, we get so caught up on doing things right and clean the first time, that we fail to realize that it's not code we're delivering, it's a solution to a problem.
I think of coding as I would writing a paper:
When writing a paper, we start somewhere, sketch out ideas, outlines, etc. It won't contain all the details or have any finished look to it-- it's essentially a first draft, followed by a second, and so forth. Much will be rewritten, replaced, and/or even removed along the way to a more refined and finished paper. (Obviously this analogy doesn't go so far as to say that code is ever truly ever finished or final like a paper.)