If you have floating or surface-reaching plants (i.e.: Cabomba, Vallisneria, etc., etc.), or even just some plastic plants floating on the surface, the fry will instinctively hide among the leaves near the surface. I always move the fry to their own area as soon as I find them, but I've had fry survive in the adults' tank for several days before I find them (hiding places can also work against the breeder. ;p)
So I've always just left pregnant females where they are.
Antony, is it just your molly's belly that's getting bigger, or her whole body? How long have you had her? Did you get her from a store? Have you been keeping her with a mature male? When I bought one of my original female balloons, she already looked ready to pop any day, but she was the last of my females to give birth--over 3 months after I got her.