Unity Navmesh on randomly generated dungeon?

I'm currently working on a 3D "Binding of Isaac" style game in unity. There a rooms that get generated randomly and you have to clear each room to advance farther. Since I'm working with 3d normal 2d top down movement (WASD and aim with mouse) turned out strange with the walking animations I have so I decided to switch to click-to-move controls instead. The problem is I can't figure out how to get the navMesh on the room prefabs that get spawned in game. I'm using an asset called "Dun gen" which has a whole bunch of tools to generated dungeons. If anyone could help me or suggest any other method of movement for a top down game that I could use. I would greatly appreciate it. There isn't really much to this question so I'll just end it at this.