Trump will have to appoint an attorney general and they can prosecute Hillary Clinton. She would be afforded a trial but she would be brought in, fingerprinted, and have a mugshot which would be pretty embarrassing. So yes, Trump can certainly do it pretty easily.
The problem is that it would be seen for what it is...the President of the United States locking up a political opponent. However, I think that Donald Trump wouldn't lose any sleep over doing something like that. With a Republican controlled House and Senate, he would not even be impeached.