For extracting the fundamental frequency of the melody from polyphonic music you could try the MELODIA plug-in: http://mtg.upf.edu/technologies/melodia
Extracting the F0's of all the instruments in a song (multi-F0 tracking) or transcribing them into notes is an even harder task. Both melody extraction and music transcription are still open research problems, so regardless of the algorithm/tool you use don't expect to obtain perfect results for either.
