Thomas Roxburough brain is preserved in a jar and he can use the Matrix to communicate.
In 2070+ they can clone whole bodies.
Why is is brain still in a jar?
Technically, Roxy is a mass of organic fluid in a tank that somehow manages to keep sentient.
As for why he's still in the tank? Well, Roxy boy has always been something of a cutthroat corporate type. Back in the days when the megas openly went toe to toe with eachother (rather than proxy fights like Desert Wars), Roxy was responsible for unleashing a nasty little virus against another corporation as a test run for knocking out a rival. Unfortunately for everyone, that virus escaped into the Matrix, and started burning everything to the ground. We call that the first Crash, by the way. Now, during the Crash, the Echo Mirage team went up against the Virus, and got their asses handed to them, before they figured out how to fight it. One of the fatalities was a hacker named Alice Haeffner. She became Alice of Wonderland, the first e-ghost in the Matrix, alongside Mirage, the first AI. And Alice decided to carry a very, very personal grudge against Roxy. So any time he gets close to figuring out a way out of the tank (or any other way to improve his life) Alice goes all Jabberwocky on it.
Now, no one's seen Alice since Jormungand rolled through, but that doesn't mean she isn't around somewhere, ready to keep Roxy in his tank (at least until she can think of something worse to do to him).