Mcedit is a popular program for large scale building. Additionally a lot of players use various mods which provide things like mirrored modes(so if your structure has symmetry you do an order of magnitude less work). A lot of massive structures are built by hand though. It's not as bad as it looks to build something massive by hand if you have a lot of detail in what you are building(the best builds always have lots of detail). Stuff like westeroscraft is mostly built by hand with some mods.