It's possible to use fleece in store bought cages, but it's more work. You would need to be sweeping constantly, and the cage would start to smell sooner than with a large cage. It would require more cleanings, and therefore more laundry.
It will smell very quickly. Forgive me if I missed some history/context on your situation (if you mean for a quarantine cage) but if you plan on using it as a full time cage pet store cages really are not large enough!