Once you created a prefab source and drag'n'dropped some prefabs in your scene, you are able to edit:
To edit prefabs, you can open the tool via Tools -> Prefab Editor. This tool has 2 parts:
Note: Undo/redo is not yet supported and will be available in future version.
Once you have opened the prefab editor and selected a prefab in the scene graph, the tool will be updated and show you the selected prefab hierarchy and the live preview. In the prefab hierarchy, you can delete the unwanted nodes (right click -> Remove).
Once you removed a node, ONLY the selected prefab will have its node removed from the scene. If you want to globally remove a node from all prefabs, you have to edit the source prefab object.
In some cases, you would like to remove a node from the source prefab and apply the hierarchy modification on all already instantiated prefabs in the scene. To do that, just select the prefab asset in the assets panel. Once selected, the prefab editor will be updated.
From now, you are editing the source prefab object. Once you remove a node from the prefab hierarchy, ALL the instantiated prefab in the scene will have their related node being removed from the scene.
This tool is the first version of the prefab editor and some features are incoming: