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How to create a scientific illustration in 3D with Illustrator

Learn how to take your scientific illustrations to the next level?

Life as a researcher means spending a lot of time making figures. And we’re not talking about your salary 💲💲! We’re talking schematics in a paper, poster or graphical abstract!

But if you aren’t a graphic designer, how do you make stunning scientific visuals?

Well, if you want to stand out and go the extra mile.

We say, go 3D!!!

Go big or go home, right?! 😉

Let’s LEVEL UP your scientific illustrations! 🙌 Follow along and learn how to create beautiful scientific illustrations in 3D with Illustrator.

3D with Adobe Illustrator

Let’s talk about 3D

A 3D object extends into 3 dimensions, that is, the X, Y and Z-axis (or length, width and height respectively). Whilst a 2D object remains within one plane, or 2 dimensions, with only length and width.

Now we can trick the eye and make an object appear 3D by strategically placing 2D shapes. Take these cubes, for example, one is 3D and one is 2D, but you can barely tell them apart.

That is… until I start to move, and rotate them.

Now the 3D appearance becomes clear!

You can see how using perspective and placing 3 squares together can create the appearance of a cube. If you have been using Adobe Illustrator for a while, you will know that the 3D effects have been pretty dismal and difficult to use. Because of this, many designers would opt to create 2D objects in a perspective that made them look 3D.

But I am here to tell you that the latest 2022 update has made them FABULOUS 🙌🏼 and will have you singing from the rooftop with how EASY it is. 🎉🎶🎉

Learn about 3D effects in Illustrator

So now let’s talk about the awesome 3D effects Adobe Illustrator has to offer.

Okay just quickly can I just say that my favourite part about the new update is the real-time 3D preview, 🙌🙌🙌 allowing you to tweak properties like depth and volume and see the changes in real time, so you can tinker until you are happy with the look. #winning 🎉🎉


This effect flattens an object into a plane. A plane can be thought of like a flat sheet, or a piece of paper 📄. It can be turned over, rotated and flipped, but does not have any depth.

Technically, a plane is not actually 3D, but what this feature allows is for the simulation of that plane in 3 dimensions.

Adobe Illustrator Plane


This effect is sooo easy and oh so handy 👏 !! It adds depth to a 2D object, extending it into the 3rd dimension.

You can change the amount of depth and even remove the cap if you want a hollow look. This is how we created the cube above ☝️ and is great for lifting things off the page and creating dimension. Yay for inbuilt shadow and lighting! 🙌🏼

Adobe Illustrator Extrude


Revolve is one of my favourite 3D features 😍. Whilst it is a little more complicated to explain, the possibilities are endless.

This feature effectively sweeps an outline in a circular direction to create a 3D effect. Depending on which direction the object sweeps, it can change the shape of the 3D object produced. Take this triangle for instance, when you revolve around the left edge, you get a cone shape, whilst you get a cylinder if the offset direction is set to the right edge 🤯.

How cool is that!!!

Adobe Illustrator Revolve


Inflate, another awesome effect with so much potential! 🤩 In essence, this feature inflates the object like blowing up a balloon. 🎈

You can either blow up just one side to create this dome look, or you can inflate both sides to give a more rounded, ballooned effect. You can also play with the depth and volume to create so many different 3D objects… Amazing!

Adobe Illustrator Inflate

Want to have a play with these awesome 3D features, but don’t have Adobe Illustrator. 😢

Why not try it today with a free trial. Check out the whole suite of Adobe programs here.

3D with Illustrator

Let’s get started!

For this tutorial, we are going to create an atomic model representing Carbon, in its most common isotope, Carbon 12. For simplicity and aesthetics, I am going to use the good ol’ fashioned Rutherford Model. ⚛ This model has been around for over 100 years (est.1911) and is probably the most iconic science icon ever; there is even an Emoji for it !! 😂

To follow along with each step, you will need access to Adobe Illustrator with some knowledge of the software and tools. Are you new to Illustrator and want to learn some of the basics? Why not check out our blog on perfecting 2D illustrations first!

To make things easy, let’s set up your work space to be the same as mine. Open up Adobe Illustrator and create a new A4 workspace. Then open up the Painting Workspace 🎨 and the Advanced Toolbar to view the same interface as below.

Adobe Illustrator tutorial Painting workspace
Adobe Illustrator tutorial Advanced toolbar

Any useful keyboard shortcuts will be indicated in brackets ( ). Command ⌘ (Mac) will be synonymous with Control CTRL (Windows PC).

Remember to save as you go! 😉

Protons, Neutrons and Electrons

Alright let’s talk science for a sec! A carbon atom has 6 protons, 6 neutrons and 6 electrons, all of which can be represented using a sphere. Easy peasy! So let’s start there.

As always with Illustrator, there are multiple ways to achieve the same outcome. To create a sphere, I personally like to use Revolve on a semicircle, but feel free to use Inflate on a circle instead.

To start with, draw a circle using the Ellipse Tool (L). Make the circle 60pt x 60pt.

Adobe Illustrator tutorial Circle

Using the Direct Selection Tool (A) select the left-most anchor point and delete it. This will remove the path in between the remaining two anchor points, leaving a semicircle.

Adobe Illustrator tutorial delete Anchor point
Adobe Illustrator tutorial semi-circle

Now for some fun, on the right-hand side you will see the 3D and materials panel. Select Revolve within this panel, and watch your semicircle magically turn into a sphere.

Wasn’t that easy!! Thanks Adobe. 😉

Okay okay, I know it kind of still just looks like a black circle 😂 but I promise its a perfect 3D sphere.

Handy tip: If you end up with a cylinder, change the offset direction to the other edge.

Adobe Illustrator tutorial 3D sphere

Protons and neutrons are roughly the same size in diameter, so we can simply duplicate our sphere here. To do this, you can either use trusty Copy (Command + C / CTRL + C) and Paste (Command + V / CTRL + V) or drag the object whilst holding down Option/ALT.

Electrons on the other hand are about 1800 times smaller than protons and neutrons so after you duplicate, resize to create a smaller sphere.

You should have 3 in total, one for each subatomic particle.

Adobe Illustrator tutorial 3D

Now to add some colour! 🎨

Hmm but what colour is a proton?? 🤔

Technically, protons, neutrons and electrons don’t actually have a ‘colour’. Colour is determined based on the wavelength of the electromagnetic wave the object emits or reflects. But protons, neutrons and electrons are smaller than a wavelength and therefore can not be seen, but I digress. Sorry! Isn’t science fun. 😊

The point is, be creative, experiment with colour! 🌈

I am going to choose purple for a proton, blue for a neutron, and red for an electron.

Adobe Illustrator tutorial 3D coloured sphere

To assign a colour to a 3D shape, you can use the same method as that for a 2D shape, select the object with the Selection Tool (V), and assign a Swatch. But in this case, we have to assign the Swatch to the Stroke (X) of the object, rather than the Fill as that is the part being used to create the 3D effect.

Illustrator has some pretty cool functionality, under the Materials tab, in the 3D and materials panel, which allows you to add dimension and texture to your 3D objects. We will briefly touch on this later, but if you’d like to have a play, I invite you to explore this section here using one of your spheres.

Drawing the nucleus

Okay, now that we have our three subatomic particles, let’s create the nucleus.

For the nucleus, we are going to have a tight pack of 6 protons and 6 neutrons.

To make the nucleus look neat, I suggest drawing a larger circle as a guide. Use the Ellipse Tool (L) while holding down shift, create a circle to the dimensions of 150 pt x 150 pt and give it a bright Fill (X) colour such as yellow. Then send the circle to the back, by right-clicking on the circle, then Arrange, then Send to Back (⌘]).

Adobe Illustrator tutorial 3D nucleus

Then place the neutron and proton within the circle on the border edge, starting at the top.

Adobe Illustrator tutorial 3D nucleus

Next, duplicate the neutron and place each copy on the border edge, working your way around the circle.

Adobe Illustrator tutorial 3D nucleus

Once you have a total of 12, delete the yellow circle guide 🙂

Adobe Illustrator tutorial 3D nucleus

Then change the colour of 5 spheres to blue, to represent a neutron. The most efficient way to do this is to select all 5 spheres, and use the Eyedropper Tool (I) to select the existing proton. The existing colour properties from that object will be copied onto the selected objects.

Adobe Illustrator tutorial 3D nucleus

Lastly, group the existing protons and neutrons together to secure your nucleus. To group objects, select all objects with the Selection Tool (V), right-click and click on Group.

Adobe Illustrator tutorial 3D grouping

Drawing orbitals

For the next part of the Carbon atomic model, we want to create 2 orbitals. Each orbital will have 2 electrons evenly spaced as dictated by the Rutherford model we chose. To do this, we will use a ring to connect the electrons and represent an orbital.

So let’s create an ellipse using the Ellipse Tool (L), and have it encompass the nucleus we just created. Rotate the shape until you are happy with the location. Then let’s add an electron at either end, by duplicating the red sphere.

Adobe Illustrator tutorial atomic model

Adobe Illustrator tutorial atomic model

Now we want to create the effect that the orbital is going through the electron, like beads on a string, so we want to cut the ellipse into 2. To do this, let’s add some additional anchor points ⚓️ using the Add Anchor Point Tool (+). You can also access this by holding down the Pen tool, which will reveal a drop-down menu for the Add Anchor Point Tool. By default, the Toolbar only shows the Pen tool.

We want two new anchor points at each end.

Adobe Illustrator tutorial add anchor point atomic model

Then delete the middle anchor point by using the Direct Selection Tool (A), this will remove a small segment from the end of the ellipse. Do this at both ends, and you will end up with two half circles.

Adobe Illustrator tutorial delete anchor point

Select one of them and go to the 3D and materials panel. Select Inflate within this panel, and change the Depth to 2.5, the Volume to 7% and the Stroke to 2.5.

Adobe Illustrator tutorial 3D effect inflate

Then under the Materials tab, in the 3D and materials. Select the Gold Natural material, this replaces the need to choose a colour. Repeat for the other half circle.

Adobe Illustrator tutorial 3D Gold natural material

Feel free to zoom in on the electrons and fix the points of the orbital using the Direct Selection Tool (A).

Adobe Illustrator tutorial

Duplicate another 4 electrons. Then group the two orbital halves together and duplicate.

Handy Tip: At this point, it can take a while for objects to render depending on the

complexity of a 3D object. So you’ll have to be patient when copying and pasting.

Adobe Illustrator tutorial atomic model 3D

Next, rotate the orbital to give the overlapped ‘X’ look

Adobe Illustrator tutorial 3D atomic model

Then using the same method above, cut each half of the ellipse into 2 by adding additional anchor points using the Add Anchor Point Tool (+), followed by deleting the central anchor point. Lastly, arrange the final two electrons in the correct spots.

3D Atomic model Adobe Illustrator

And that is it! A simple but beautiful 3D image. WOO 👏 👏 👏


  • Go a step further, add a background, and some smaller blurry carbon atoms in the background to give a shallow depth of field impression.

  • Try to create a 3D graphic of your research and use it in your next scientific poster, presentation, or graphical abstract. You never know you might even be featured on the cover of a journal.

  • Design a 3D image like a lab logo for infographics and presentations. You’ll become the lab legend overnight!

Or just have fun with it and play around in Illustrator using your new 3D skills. Share your creation with us in a DM or tag us on social media, we’d love to see your creations!

Don’t have the time, need something now?

No problem, let us do the hard work for you! 😉

At Animate Your Science we can create an eye-catching 😍 and accurate scientific illustration for your upcoming paper, poster or presentation.

Want more? Our team of science communicators and designers can turn your research into a show-stopping custom animation.

Contact us now to discuss how we can help you to unleash your impact!


Dr Khatora Opperman

Dr Juan Miguel Balbin

Dr Tullio Rossi


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