To flatten a part of your mesh:
- Go to edit mode.
- Select the bits you want to flatten.
- Change the pivot point to "Active Element" through the pivot point menu.
- Deselect and reselect an element (vertex/edge/face) that represents the height for your flattened selected. This will set this element as the active element. The entire mesh will be flattened to this height.
- Scale to 0 on the Z axis via: S-->Z-->0.