Styrofoam flip-top boxes (or hinged-lid boxes) have almost entirely replaced "doggy bags" in my neck of the woods. In some restaurants the server does it for you (or offers to) and in others it's do-it-yourself. If you ask for a "doggy bag" everyone will know exactly what you mean, and will bring you a box. In most cases where the restaurant accepts "to-go" orders, the same boxes are used.
If the server sees that you've finished eating and have left a substantial amount, he/she may ask, "Would you like a box?", or "May I box that for you?"