In my opinion, I back science as my reason of existence. Magick to me is just science that we have yet to figure out yet, as science knows we all vibrate with an energy, but doesn't know why. Magick itself to be is just that, the energy we personally use directed towards a specific goal.
We do not worship dieties for they to us do not exist. Spirits maybe, it depends on who you ask. We as humans have the technology to see ghosts and other things of such nature, we just cannot explain why they occur or what they are, so working with spirits is very possible being an Atheist (unless you claim the spirits are in direct workings with a god/dess, then it goes out the door).
As for a pentagram, pentacle, hexagram, whatever symbol one chooses, it is just that, a symbol. A symbol simply is a representation for something, such as the 5 points representing 5 elements. That is all. Some can claim a magickal backing, others say it's just a cool picture. Either way, symbols are just symbols, and has nothing to do with Atheist at all. If you personally want to use a pyramid instead of a pentagram that is personal choice to do whatever with.