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It gives the greatest ability to manage scan workflows for busy departments with features to take the manual steps out of your image capture engine.
In this context, does "take the manual steps out of" mean "remove manual steps from image capture engine so that the user can work efficiently"? I am not sure if it means "take steps outside something (which means to take action not in, but outside)" or "take steps out from something (which means remove or take away)".
Your first inclination was correct!
To take steps means to undertake measures or to do something. Taking the steps out means to remove steps.
In the sentence, they are removing things that have to be done.
The sentence is advertising some form of automation that saves the user from having to perform a series of actions. In theory, this should increase efficiency and productivity.
