(via Desktop Project Part 8: From filament to prominence | Bad Astronomy | Discover Magazine)
Normally, filaments look dark and prominences look bright, even though they’re made of the same stuff. That is, when plasma flows along the magnetic lines above the Sun’s surface, it looks dark against the background of the Sun itself, since it is cooler, but bright against the background of space, since it is much hotter than empty space.
However, if you use a really good, precise Hydrogen-alpha filter and darken the Sun a bit, you can get a picture like this, where it is more obvious that the filaments and prominences are the same thing: a massive amount of plasma above the chromosphere of the Sun.
Credits: Tom Wolfe, used by Phil Plait on Bad Astronomy by permission.