For enemies in the level to navigate obstacles they need a map 
Add a NavigationRegion3D node as a child 
Add all nodes that you want to be part of the map 
I added the floor and all level objects 
Select the NavigationRegion3D Node 
In the Inspector add a New NavigationMesh 
Now create the map of the level 
by hitting the Bake NavigationMesh button 
This will now serve as a map of the level for enemies to find their way around