It might take some practice to really get the best effects.
The best way to get it to work is by focusing on your breath. As you breathe in, count "one, two, three..." and as you breath out, "three, two, one."
I found that when I started using binural beat programs, clearing my mind was the biggest challenge, but once you begin practicing focusing your mind, it will get easier.
Sometimes it helps if I sit wondering what my next thought will be. This separates yourself from your thoughts themselves, and makes you realize that you are in control of your thoughts and not the other way around.