A larger matrix like this 16 x 16 x 16 LED build, has a total of 4096. This would be a nightmare to drive with plain RGB LEDs, even with cunning multiplexing, but luckily you can buy indexable ...
If you want to create a large display with a matrix of LEDs, it’s a relatively straightforward ... He also goes into some detail on the multiplexing circuitry he used to drive the whole array ...