If I get from this that you logged in over the network as root then you made a mistake.
What you can find on your machine depends on a few things like if you have off-site backups, what your distro+version is, what services were running, what you installed in terms of intrusion detection / integrity checking, what root was allowed to do between compromising the host and you restricting access to it. What you can do now is listed in the post here:
http://www.linuxquestions.org/questi...96#post3608496. But please reply in this thread, not there.