Just to clarify, who chooses what to remove?The opponent or the Marines?
If it isn't explicit, the owner of the card always gets to make all decisions.
In the case of Fury of the Ultramar, the marine player tells his opponent "remove one shield die" or "remove 2 shield tokens". The opponent doesn't get to choose which "option", the marine player does.
Contrast this with the Marine card "Break the Line", where the opponent gets to choose which card he must throw away.