Step 0:
Uninstall that tomcat6 package you installed.
Step 1:
Verify tomcat is running somewhere by running a port scan on your server.
nmap -sV servername
Step 2:
Now that you have the port, use lsof -i :portnumber
to find out which nefarious process is giving you grief.
Step 3:
Use the PID from lsof
to find the exe and how it was run:
readlink /proc/PIDNUMBER/exe
cat /proc/PIDNUMBER/cmdline
Step 3.5:
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.
Step 4:
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.