Select all of the vertices that you want in vertex mode. Then you scale them on the axis that you want to flatten them by. You will scale towards the area that you want flattened.
For example, if there is a box where the top is not flattened, then you would scale along the verticle axis and scale down, towards the top of the box. Once flattened, you can then move these vetices around to the desired spot.
If you play around with the scale of vertices, you can find some interesting results that will help you in modeling later.