How Do You Make A 3D Atom Model Of Oxygen?

I would use rubber bands to illustrate energy levels, pennies to represent the orbiting electrons, and then red and blue marbles for the protons in red and neutrons in blue consistent with the image of oxygen attached.

Well first figure out how many protons and neutrons are in the element and then make the nucleus, protons, neutrons, electrons. And there orbitals. For the nucleus you could get a styrofoam ball and cut it in half and then put painted golf balls inside it to represent the neutrons and protons. Then get some wire or a coat hanger and spin it around the nucleus with beads on it to represent the orbitals and electrons.

You can make a 3d model of oxygen atoms by using the colored styrofoam balls which are held together with some toothpicks or straws. Hope it helps.

Back in the dinosaur days, we made them with a wooden base which supported a wooden dowel, with a ball on top to be the nucleus.  The ball had colored thumb tacks to indicate protons and neutrons (had to be the correct number of each).  Then a stiff wire like a coat hanger was pushed through the center of the ball.  The wire held circular orbits with beads on the orbit wires based on the number of electrons for each element.
The instructor liked the girls so he gave them elements with the least orbits and the boys got the ones with many orbits and electrons.

There is some good 3D (but not really) software out there, some free, some Very expensive. 3D modeling is often done in lieu of actual chemistry to see what is possible, likely. 20 years ago we had to reserve time on a VAX computer to do these simulations but now days any new PC works well.