Worlds in Starbound are a mixture of procedural and hand-designed content. While the terrain height and caves are procedural, some individual elements on these worlds, dungeons, microdungeons and missions, are assembled from parts that we’ve designed using a tool called Tiled. Having a good understanding of how to use Tiled is essential to being able to create mods that add more of this type of content.
Tiled is a general purpose tile-based map editor, designed to support map formats for many types of games, not just Starbound. It has a ton of features (not all of which Starbound supports), and is generally very easy to use (although its generality can sometimes be non-optimal for specific projects like Starbound).