I made an original prefab to load prefab into MAST.

And I've  made my stage.

When I use eraser, all of object in the scene are deleted.

If I want to erase any object  by using original prefab in MAST, I have to click the object and delete one by one?

that sounds scary, I've only just started using this and haven't deleted anything yet lol, I'll test this in a sec and see what happens.

normal delete works fine, so you must mean something else. im using unity 2019.2.0b9

Are you using the merge tool before attempting to delete the objects?  I can't imagine that happening, but I always explore every avenue!

Does the parent gameobject for each of your prefabs have a mesh or collider?  This would cause the MAST Holder gameobject to be deleted.  This may be on me if it's just a collider in the parent causing the issue.  I've really only tested with mesh colliders in the children.  If you use MAST tools Create Prefabs from Models, it will create more MAST-friendly models in the meantime.

Let me know if this helps!

It works!

The cause is that my way to make prefab.  

I made prefab that has no parent.

Now I make prefab that has parent.

And I make my Stage.

When I erase one of object in the stage, It works that only one object are deleted.

This is that I hope.

Thank you very much for your answer. That helps me.

And thank you for giving a great Asset.