Unfortunatly, those are spots where water get at over time which probably means it is not surface rust.....As mentioned those are crucial spots to have rust.....I can't remember who said it on here but "Once you get rust in those crucial spots, it is like cancer, never goes away."
Hey but try sanding it down then some bondo and you may have some luck.....
Past: 1998 323is (E36)
1986 325e (E30)
Present: 1997 Jetta GLX VR6
2004 325iT (E46) (pops)