Easiest way to do this is to kill all programs run by the user. You could also just kill the programm the user uses to connect to your box.
Or if you got his ip adress. Deny connections from this ip. Either using iptables, or hosts.deny/allow.
You could check out some security-papers and read the section about "What to do during a compromise" or similar headline.
Hope this helps
--zhjim--
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