Printing the filament like in the linked article is essentially in 2D (not really, but for this point it's close enough). So if you have 2 colors, you can first

Printing the filament like in the linked article is essentially in 2D (not really, but for this point it's close enough). So if you have 2 colors, you can first print all color 1 segments, and then manually switch and print all color 2 segments. In a real object your print is 3D and consists of layers that are ~ 0.1-0.2mm high. In a typical multicolor print each layer has several colors, and you have to finish a layer before printing the next one. So you have to switch between all colors that are present in each layer.