Deleted Program Files Still Running

I deleted an application via AppCleaner but some of it's files still running on activity monitor, under root user. I can not find where the files are even when I get information and follow the path under the root user. Is there another route I can go?

What program was it?
As you can see, the app cleaner programs don't always work well.
There are very few places that an app can leave their droppings that can do any harm. The most common places that an app can run at login or startup is in the following folders:
/Library/StartupItems (this one is the old way, but still used).
/Library/LaunchAgents (these run when someone logs in)
/Library/LaunchDaemons (these run when the system starts up)
~/Library/LaunchAgents (run when particular user logs in)
~/Library/StartupItems
The / means the root (hard drive) folder
The ~/ means the user home folder.
Finally, they can install in your Login Items which you can get to from the Accounts System prefs.
As Lex mentioned, you may need to stop the process before you can empty the trash (use Activity Monitor from the Utilities folder).
If an app installs stuff like that, they should provide an uninstaller and you should use that.
If it doesn't, most other droppings may be found in the Application Support folder (in both the main Library and the user Library), and the user Preferernces folder.
Generally, most apps follow Apple's naming convention of reverse domain naming (ie com.apple.appname).
Except the StartupItems folders, you should find something with a com.companyname.programname.plist.  Delete it and logout and back in or restart if it was in the main Library. In StartupItems, it will be a folder with any name they decide to give it. Likely something with the name of the program.

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