Uninstall that tomcat6 package you installed.
Verify tomcat is running somewhere by running a port scan on your server.
nmap -sV servername
Now that you have the port, use
lsof -i :portnumber to find out which nefarious process is giving you grief.
Use the PID from
lsof to find the exe and how it was run:
Depending upon OS, check to see which package your exe belongs to. On apt-based (Debian/Ubuntu), that'd be
dpkg-query -S `readlink /proc/PIDNUMBER/exe`
On Gentoo, use
equery belongs `readlink /proc/PIDNUMBER/exe`
And on rpm-based (Fedora/RHEL/SuSE/whatever)
rpm -qf `readlink /proc/PIDNUMBER/exe`
And if it isn't an OS package and you installed it yourself, hopefully you already know what it is.
Now, armed with the might of cold hard fact, upgrade that package to within an inch of its life! If the scan found a major vulnerability you missed due to a lax security upgrade procedure, fix your update procedure.
And if any of these steps have failed, talk to the (isScannerOpenSource ? community on IRC : support hotline). See if logs can tell you where the scanner went wrong. And possibly get rid of it and try a new one.