Depends what you are trying to lower. Units cannot be lowered unless a flying unit, but it takes trigger work to lower/raise them.
Doodads on the other hand only require you to select the desired doodads that you want to raise and then do the following:
Hold Control (Ctrl) and then press either Page Up (To raise the doodad(s)) or Page Down (To lower the doodad(s)) to adjust their height. Let go of Ctrl when you are done.
Terrain on the other hand, in general, is not allow you to raise or lower things such as Cliffs, Water, Sky, Fog, or Weather. However you can create hills and make them steeper, taller, and bulkier if you wanted to with the "Raise" tool in the Terrain Palette. You can also create ditches or lower the high-lighted area of terrain with the "Lower" tool in the Terrain Palette.
~Craka_J