There are several companies that offer tours from Lima. Someone I know did one (using AeroCondor if I recall correctly) and they fly from Lima to Ica, where you transfer to a smaller plane for the flight over the Nazca lines.

Alternatively, there are tours that go south by bus, but it's a long ride. You might also look at overnight tours that include time in Pisco or Ica or Paracas (for Islas Balleastas). Some of those go by bus, some by private car.

I'm actually planning on going to Nazca directly from Cuzco by bus, but that's a 14 or so hour overnight trip so I don't particularly recommend it.