Well, he can already order experiments on strangers. And since I doubt Lex is going to learn Clark's secret, my guess would be he's going to experiment on Lana.

Comics!Lana knows Clark's secret. She learned it back when they were both still in Smallville. He took her flying and told her the truth about himself before leaving for Metropolis and actively starting to be a hero. Comics!Lex actually kidnapped and tortured Lana to find out Superman's real identity. When she wouldn't break, he ordered her released.

So. Lex experimenting on/torturing Lana has precedence in the uber-canon. Personally, I'd probably enjoy him torturing *Lionel* more, but there you go!