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?
It's a combination of things.
Originally he was diagnosed with a serious auto-immune disorder whereby his own body defences was attacking healthy tissue.
Realizing he had few options he tried out some of the earliest experimental geneline treatment with mixed results.
It did what it said on the tin, stopping the body from eating itself.
However it also left the body cells constantly redifferentiating, so his liver might suddenly decide to become muscle tissue and so on. (Aztlan 62-64)
Now obviously his brain has remained more or less intact, otherwise he wouldn't be able to work via the Matrix, but even then there is some who think even his brain is a bit wonky.
Roll ahead a few years and Roxy has a plan to get a new body via a ritual transfer, but that plan gets sabotaged though his foes leave him in the vat rather than finishing the job because it seems more fitting he lives on to suffer. This is touched on in the Dragon Heart Sage SR Trilogy novels.
As for a new clone body, I imagine since the original treatment modified his geneline, any attempts to use the tainted cells for making a new body carry the same problem.
They
should be able to go into a sample and rip out the bad sections and rewrite the coding to make something that could work, but maybe it is so invasive that any 'clean' sample is also incompatible with his brain so he would have rejection issues.
Remember he started out with a really nasty auto immune system that
ate healthy organs that were his own, it's only because they keep changing that they fool his defences.
Plus toss in various parties and powers in play that continue to keep an eye on him that would probably sabotage any attempts on that front.