Use racketeering laws to go after them.
That was what happened when Democrats used RICO to go after anti-abortion groups.
I believe that is what Trump has in mind. The RICO law offers a wide range of remedies such as civil injunctions, asset seizures, and criminal prosecutions based on participation in a criminal enterprise. In this instance, Antifa will be described as a domestic terrorist organization in order to explain that in violating criminal laws, it aims not at material gain like the Mafia but at causing political disruption and intimidating political opponents. This will help to identify RICO predicate offenses and to seize assets.