Regarding someone who has separated teruma and maaser with a t’nai on Shabbos, is he allowed to handle what he has separated or is it muktzeh

If the produce from which he separated teruma or terumas maaser was tevel vadai or safeik tevel, the piece he has separated becomes muktzeh since it’s forbidden to eat, and therefore one may not handle it on Shabbos. (The same would apply to the piece separated for hafrashas challah done with a t’nai.) However if the separated piece is still in his hands, he does not have to put it down immediately but can place it wherever he wishes. If one is separating teruma and maaser only lechumra, from produce purchased with a reliable hechsher, the separated piece is not muktzeh even for those whose custom is to take maaser again.