A father has a job checking the bunker reserved for important government figures in the middle of nowhere. He brings his daughter along to spend some quality time with her. They stay in the lavish bunker, but while they are underground, aliens attack with a weapon that breaks carbon bonds. They find the tires and other rubber and plastic parts in their truck (van?) have disintegrated. As well as killing nearly all of humanity, it nearly sterilizes the soil, killing off all biological matter. Everything seems hopeless until they receive a signal from somewhere close to Santa Fe with other survivors.
That was the first third of the book. The second third follows their descendants reseeding valley by valley. They have to build the ecosphere from the ground up.
The final third takes place many years later, when humans have rebuilt, and start negotiating with the aliens who wiped out humanity.
The book is from the 1980s or 1970s, not sure which. I don't know the title or author. It's a young adult novel. I also remember a short story in another book by the same author in the same "universe"