We're going to use CSG geometry to rough out our level. It's the in-editor 3D modeling tool. While you could rough out the level in a 3D application such as Maya, Max, or even AutoCad, CSG gives you an incredibly fast turnaround when you begin working out the gameplay of your level. It's much easier than going back-and-forth between the different software packages.
That said, CSG isn't good for anything very detailed. It's expensive, it's hard to work with, and is prone to errors if the geometry gets too complicated. For this reason, it's great for prototyping since you don't want to add much detail in the early stages. It's also suitable for some simple geometry in the final level, as you can see in some of the epic's maps.