For the most part, it's not about clean vs. unclean food. It comes down to energy. Calories are energy. If you're putting more energy into your system than you are expending, then you're going to store it in the form of fat (and some other things).
So step one is getting a handle on this.
How you go about it depends heavily on you and your progress. Some do well signing up for something like and purchasing a food scale. Many are surprised by how much they're eating once they get their hands dirty with the math.
Others do better by simply making smarter choices with food. So called healthy foods tend to be less calorically dense than junk food. So if you stick primarily with the healthy stuff, you're chances of over-consuming energy is reduced.
That said, I know plenty of people who overeat healthy food too.
My advice varies on the person but in general, if the latter approach isn't working for you, you're most likely going to have to resort to the former. That doesn't mean you'll be locked to counting calories for the rest of your life. It simply means you have to dive in a bit deeper until you get a better handle on things.