I am guessing this is related to an earlier question?
To run Tomcat as root...*
Assuming you have installed the tomcat6 package from the Ubuntu repository edit the /etc/init.d/tomcat6 file and change the line:
That being said...
Running Tomcat as root is not recommended in environments where it is accessible to untrusted clients (e.g. the Internet). The problem is if Tomcat or one of your web applications running within it are exploited in some manner they have full access to the underlying system. e.g. They can modify files, execute processes, etc.
Granted the chances of this are slim, but it is better to plan for the worst and hope for the best.
A more secure approach is to continue running Tomcat as the default tomcat6 user and have that call the external, chrooted process in a more isolated manner. How you do this depends on the process that is being called and what needs to occur.
If you post information on the process being called, what it is doing and why others will be able to help you identify the best way of achieving this. For example you could setup a monitor that executes the chrooted task whenever the contents of a directory change, or a local web service that Tomcat can call to run the process.