I need to distinguish fundamental frequency from harmonics. Any clue to do that?

If you are recording the music you are analysing, yourself. Record directly into a non-lossy format (like.wav) and use as high a sample rate as your software allows. Many recorders can create .wav files with much higher sample rates than the stand 44,100 hz. Some will even allow you to specify any rate you type in, so FFT friendly powers of 2 are possible.