If you’re shooting indoors, could you possible block any windows so no natural light comes into the scene? That way, you can light the scene yourself, removing any shadows with fill lights.
Why do you need a green filter on the lens? You could add this in post. This would be my preference, as it would give you perfect footage to mess with yourself. I’d be worried that a filter would degrade the image quality. It’ll also be more difficult to add any visual effects to a green image. Add them to a coloured image, then tint the whole thing green.
One other thing to think about, that could give away that you’re not really shooting in night-vision, is the “cats-eye” effect (that’s what I call it, not sure if there’s a technical term…). If you look at night-vision shots, you can often see the human retina, just like a cat’s eye. That’s because (I believe) Infra-Red light, used to shoot night-vision, passes through the eye and isn’t absorbed like other frequencies of light, so it reflect back out. A quick Google search should tell you more. I guess most people (including myself, now that I think about it) would probably look past this though, probably wouldn’t even notice…