Your office may be a mess, but you can get into an even bigger mess if you decide to go to battle with your boss over this request. On one level, if you are performing well, the fact that your office is a hovel should not matter a great deal.
However, there are circumstances where the cleanliness and orderliness of your office can make a difference. For example, you said that you occasionally have to step over a pile or two. That instantly points to a safety problem and the increased likelihood of someone tripping and falling when navigating in your office, and that someone can easily be you.
Although you claim that you can quickly access whatever you need, you would be able to do so quicker if your office were well-organized. This obviously does not mean cramming a bunch of files into a cabinet and then shoving the drawers closed. There are real systems to help you organize your work, and there is even a question as to why you have so many piles of paper in this increasingly paperless world of work.
By getting things in order, you will be able to find what you need even faster, and you will reduce the likelihood of doing so by accident.
| 
