with runtime() would I be able to process the list of files
The Runtime class has a method that will execute a commandline. Do you have a command that can be executed from a commandline that will do what you want?
Open a DOS window and execute a command to see if it does what you want. That command can then be executed in the Runtime class's method.
If the program you want to execute is a java program contained in a jar file and it can execute in the same JVM as the driver program, then you can call its main method directly without using the Runtime class's method.
There would be a problem that would need special handling if the called program uses the System.exit() method.