// Imports and error handling omitted for brevity.
final File file = new File("your.stem.mp4");
final String[] stemNames = {"master", "drums", "bass", "synths", "vox"};
final FFAudioFileReader ffAudioFileReader = new FFAudioFileReader();

// getAudioFileFormats(file) is an additional method that allows querying
// the file for its streams/stems.
final int stemCount = ffAudioFileReader.getAudioFileFormats(file).length;

System.out.println("Found " + stemCount + " stems.");

for (int i=0; i<stemCount; i++) {
    System.out.println("Reading stem " + i + " (" + stemNames[i] + ") ...");

    // Open stream with index i (this is a non-standard FFSampledSP method).
    final AudioInputStream in = ffAudioFileReader.getAudioInputStream(file, i);

    // Often, Stems are Apple Lossless encoded.
    // Therefore we have to convert to signed PCM; FFSampledSP is capable of doing just that.
    // If you need to decode other formats than Apple Lossless, you might need to recompile
    // FFSampledSP/tagtraum FFmpeg with the appropriate flags.
    final AudioInputStream pcmIn = AudioSystem.getAudioInputStream(AudioFormat.Encoding.PCM_SIGNED, in);
    final File stem = new File(file.getParent(), file.getName().replace(".stem.mp4", "." + stemNames[i] + ".wav"));

    // Let the audio system take care of writing the WAV file.
    AudioSystem.write(pcmIn, AudioFileFormat.Type.WAVE, stem);

    // Free resources.
    pcmIn.close();
    in.close();
}