I wouldn't-the towel will just act as a breeding ground for bacteria and possible molds. An inverted bowl with a small hole will work just fine as a hide box, or one of those plastic pet water bowls with the wide rim around the outside so that there is a space between the rim and the actual bowl itself underneath. The snake will end up soiling the towel.
Not to mention that if it gets scented by a prey item, it is swallowable. Occasionaly you hear of large snakes eating items of clothing, towels etc. Not good for the snake (or the towel).
I beg to differ, I've used towels before without a problem. It's no different than using paper towels as substrate...snakes will burrow underneath them as well. If you keep things clean than you don't need to worry about mold, excrement or rodent residue, but it is easier to have a couple of plastic overturned flower pot bases with holes in the top..wash and replace.. Towels need to be laundered (without fabric softener)! I still occasionally leave a carrying bag in with the snake....I just let the snake slither out on its own instead of reafing it out.
I've had towels in before with snakes and I also leave the bag in sometimes. But there is a big difference between doing this on a short-term basis and long-term basis. I have read enough stories of snakes swallowing things that block their intestines that I figure it isn't worth the risk -- particularily since, as you say, an overturned flower pot would work just as well (or any number of vessels).
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