It's possible that they've installed a rootkit in which case you may not be able to tell that they've compromised your computer at all. At the very least you should change all your passwords to secure passwords and disable root login and stuff like that. There are some programs like
chkrootkit or
rkhunter which can sometimes detect signs of rootkits and stuff like that, but they're not guaranteed to work on a compromised system. Someone else might have more ideas about this.