We certainly see in 3D. Our brain is wired to take the two 2D images that each of our eyes receives, and incorporate them into a 3D mental image. The brain also uses other tricks, such as relative size and speed, to create a 3D image, so that even people with only one eye still perceive more than simple 2D (though there is some loss of depth perception). Seeing only occurs when an eye receives and image and there is a brain to interpret that image. Now, you might argue (accurately) that they image projected onto the retina of each eye is only 2D, but there is more to seeing than the mechanics of the pinhole camera that is the human eye.