I bought a section of cheap linoleum type material at Home Depot. The pens are 4x4, so I would get something that's 5x5 or so. Then you can roll it up and stick it in a closet or something somewhere when you're not using the pen. It makes a good solid surface that's easy to mop up and disinfect, yet can be thrown away if it gets yucky.
If your dog isn't a big shredder, you can get the thick plastic sheeting that comes in rolls like painters use and such. You can put that as a layer on the bottom to prevent things reaching the carpet, and then just throwing a sheet, blanket, rug, whatever over top as a "base" for the pen.