I guess how I'd handle it depends on whether this is a new occurrence (perhaps in response to your work schedule changes) or something that has always happened. If it isn't new, before you put them to bed, tell them that it's time to be in their own beds, and tell them you'll take them back to their own room if they come into yours in the middle of the night. Then I'd do like another post suggested and simply walk them back to their rooms when it happens. You might plan on consuming extra Starbucks during this time :-)
If it's a new thing, it's likely because of the work schedules and they just want/need to be near you to feel comfort and security. I'd put sleeping bags or blankets on the floor and let them know they have a spot there if they need it. We did this with my 4 yr old (who goes through phases of this every few months) and it works great. I'd wait a few weeks before working on getting them out of your room completely.
Also, ask them if there's something that will make them want to stay in their own rooms -- night light, leave the door open, etc. Some friends of ours got their daughter a funky fiber optic lamp and instantly solved their problem with night time visits. There are some cool lava lamps, electronic fish tanks, etc.
Also, if they don't share a room, maybe they could sleep in the same room for a while.