Well, while you won't find a Green anole burrowing, it's still nice for them to have substrate, preferably something that looks like soil or leaf litter. I'm keeping a baby Green on a moist Bed-A-Beast and Calci-sand mix, and it's mostly for security reasons.
If there's a reason that substrate is getting in the way or has become a problem, it's not so bad. I mean, the tank will be cleaner (assuming it's regularly cleaned) with a bare-bottom tank... just make sure it's very lush with live or fake plants. You can also put dark paper *under* the tank (or put it on a dark surface) and cover the backside of the tank with dark-colored paper or a background. As long as the anole feels safe and protected (able to hide), everything should be fine.
Their claws are probably better off on glass then they are on butcher paper, and they barely use the ground, anyway. It's easier to mist the plants in a tank without paper on the ground, as well.
Clean the tank well, I think about every-other-day would be good. Clean with a mild vinegar or very mild bleach solution and rinse very, very well. You could use dish or hand soap if you rinse very well as long as water doesn't collect on the ground where the anole might drink it.
Let us know what you do and good luck 
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