Browser window control focus

Question

I'm working on a web app that interfaces with TWAIN devices (document scanners). JavaScript sets a Java applet's boolean that triggers it to pull up the scanner interface. When the TWAIN interface is shown it is sometimes behind the browser window. It sounds like there's no way to set the TWAIN window visible, so instead I need to send the browser window backwards to be behind it. I have tried JavaScript window.blur() and also Java setVisible(false) in my applet and neither seem to work. Keep in mind I don't have any popup windows, the applet is embedded in the only browser window. I have read that JNI is capable of this but cannot find any examples. I am capable of using JNI because my applet is signed, although I'd prefer a JavaScript solution as it would be easier to implement.