One of the English language's most basic idioms, "I see" (without further context) does not mean actually, physically seeing something with your eyes; it means, seeing something with your mind. Or rather, your mind sees the logic of something.
Example: "So when I rebooted the computer, that solved the entire problem." "I see."
This should not be confused with, "I see that..." because this is used in a far more literal way.
Example: "I see that you brought your lovely wife Michelle... please, come in!"
This is not an idiom.