Meditation, japa, prayer all mean the same thing, finally. They are only various ways of expressing one and the same thing. Ultimately, your desire must be for God only. We were mentioning about perfect thought. Perfect thought is God-thought, and that only is the way of purification.
Desires are all selfish and they have to be converted into unselfish desires in the next stage.
Then, the unselfish desires also should cease in the Universal desire for God. The desire by itself is not bad. It all depends upon to what object you are directing it. If it is directed to your personal physical gain only, it is selfish desire. If it is directed to the welfare of all people, it is unselfish desire.