You don't need to worry about the fact that it's a USB drive; when the user inserts the device it is recognized by the OS and shows up as a mounted drive in your filesystem. Then you can just use java.io.File and friends to access it. Additional tip: use org.apache.commons.io.FileUtils as a handy toolkit to make many common file-related tasks easier.
If you need to detect the new USB device automatically in Java, that's a bit tricky. See this question.