Trading money in Japan is a simple and painless procedure. There is little variation in the exchange rate, almost no black market for currency, and fewer people looking to take advantage of a naive tourist. The only possible pitfall is the language barrier. Don't count on the person on the other side of the window speaking English, because he may not. This shouldn't interfere with the process of exchanging money, unless you need to ask some questions while you do it.
Things You'll Need
Find a place that accepts foreign currency. There are exchange windows in the major airports. Most big banks also will offer currency exchange services, and there are a few businesses in the big cities that deal exclusively in money trading. Most will post rates right up front. Your hotel desk also may offer these services, although the rate may not be as competitive.
Have your passport ready; they may ask you for this when you exchange money. Some places may require at least some form of identification, and likely will not accept any foreign ID other than a passport.
If you're in a bank and can't find the exchange counter, you can ask by saying "ryougae-jo wa doko desu ka?" (Where is the exchange counter). Many banks are large and you might have a hard time finding an employee who speaks English.
At the window, you can pretty much just hand over your money and they'll know what you want to do. But you can try saying "I'd like to exchange money" in Japanese. The phrase is "Ryougae shitai no desuga."
You may be given a form showing the details of the transaction. Japanese citizens will likely stamp this form with a personal seal, but it is acceptable to simply sign it.
Your money will likely be handed to you in a little green tray. It's acceptable to either take the money from the tray, or pick up the entire tray to get your money (returning it when you are done). You'll be expected to count your money, of course. Try saying thank you in Japanese: "Arigato gozaimasu."