It is a little ambiguous (what exactly is a "3x3 cube") but I tried a bunch of variations and I simply could not get any Gemini models to produce the right output.
You can do it, but it takes two steps. Code is generally better to create such strict geometry (even from ambiguous prompts), while the image diffusion model is great for tuning style and lighting.
To me, beginner level coding is about being able to convert your ideas to code. That gives you a good starting point to then go deep in whatever domain of software world you want to go.
A 3 * 3 cube made out of small cubes, with a small 2 * 2 cube removed from it - https://chatgpt.com/share/69e85df6-5840-83e8-b0e9-3701e92332...
Create a dot grid containing a rectangle covering 4 dots horizontally and 3 dots vertically - https://chatgpt.com/share/69e85e4b-252c-83e8-b25f-416984cf30...
One where Nano banana fails but gpt image 2 worked: create a grid from 1 to 100 and in that grid put a snake, with it's head at 75 and tail at 31 - https://chatgpt.com/share/69e85e8b-2a1c-83e8-a857-d4226ba976...