In Goenka’s practice we were taught to eliminate all unwholesome results (Sankharas), that we have built up over our lives. Only then can the mind become completely pure.
In this long life, and even over countless lifetimes, one can never hope to let go of every unwholesome thought or act that ever happened. And actually, there is no need for that.
When you 6R, gradually the unwholesome thoughts (hindrances) weaken. In not too long a time, they finally stop altogether, at least for a little while. A Jhana will arise. Then another thought comes up and you 6R it, weakening the thought-stream again.
You progress step by step, but you only need to observe and 6R the hindrances that come up during your sit. Once a Jhana has come up, the whole concept of self starts to weaken, and the thoughts, like branches, die off. Finally, you cut the trunk of the tree with deep insight and no more branches can grow back. No more self-concepts or hindrances. Only pure awareness and being in the present.