Board Thread:Lore Discussion/@comment-5131223-20130411153637/@comment-75.75.80.173-20140419230533

Perhaps the Dwemer were so advanced, they figured out how to siphon souls or even pull them from the depths of Nirn  (  aspects of their ancestors ?  ). That, or the Dwemer could have just found rare materials similar to Aetherium.

I am doubtful the Dwemer would take the souls of Falmer, though it may depend if they were rebellious towards Dwemer regardless of where their souls are.