As I take a picture,please stand with your back against the door. does this sound natural?

It's sounds a little bit formal but it's polite and natural. ^^

You can also say, "While I take the picture, please stand with your back against the door" or "Please stand with your back against the door while I take the picture."
Personally, I think the second sentence is the most natural.

It is natural but it's not the most common way to say it. I can tell that this is similar to how you would ask in Japanese.
Usually we would ask it as a question in English. For example, Could you please stand with your back against the door while I take your picture?
It can be said multiple ways depending on the situation as well. Another natural would be to say something like "I'm going to take a picture, could you please stand with your back against the wall?"
Your way is still natural but it's quite formal sounding so if you are a staff maybe it would be common for you to use that kind of phrase but I tried to suggest some more casual alternatives.

You're welcome :)