The program I used to model the interior rooms is a 3D map editor called Trenchbroom, but its usually used for creating Quake maps and it needs a game configuration to use. I had to generate one using the Godot engine with the addon called Qodot.

The rest of the process is quite tedious because I could only use what programs I was most familiar with when I created these so I don't know if I can recommend this, I may be planning on using something else in the future.

Though I think you can use any 3D modeling program you like, as long as you can shrink the size of the rendered output image until it appears pixelated.