It's left to the imagination. Most likely infrastructure. The White House, the Pentagon, Pearl Harbor and McDonalds.

i always assumed they destroyed any ground based defenses, allowing the colony force to subjugate the defenseless population

Yeah... pretty much what the 1st reply said.

though, hitting the plant life would do it too.   Only TEC really seem to use nukes though.  I'm not sure what advent uses, but it seems like Vasari use beams which I imagine mess up everything about the planet including but not limited to average surface temperature.    I.e. it doesn't really matter where the beams hit.  They slowly draw a VERY wide belt of death as the planet rotates (which is never on a tilt for some reason) and the planet slowly becomes more and more inhospitable.

Since the planet still has 'health' even after population is reduced to zero, one can assume they have to clear out the few (less than a million) survivors hiding in bunkers and any sort of automated defenses that might be on the ground.

@ Landisaurus, why would they want to clear them out when they could use them as taxable citizens?