It depends on the game.
3D with a 2D view almost all objects are imported into the software and then just moved and rotated into place.
3rd person games all objects except the large ones are modeled and then imported.
1st person games almost every thing is made from set pieces, this is known as a modular workflow. It allows the level designers to build huge scenes by using set pieces and combining them with other set pieces.
It's important that when using a workflow like this that all three densities(Poly count, detail size and texel density) are considered hard rules, with only a +/- 10% leniency, if you allow any artist to stray too far from these lines they will create set pieces that doesn't match the rest of the game.
Here is more on modular pieces:http://wiki.polycount.com/wiki/Modular_environments
There is a mod for Fallout 4, that allows you to use all the set pieces to make your own settlements; it's a good way to see how set pieces work and all of them are made by top artists.