Use a slicer like PrusaSlicer or Cura to turn the 3d model into a GCode file that 3d printers can understand. These files work by "slicing" the model into many 2d layers, each layer made up of thousands of lines. A slicer is a program that takes a 3d model, usually a .obj or .stl file, and, to the best of it's ability, turns into thousands of these lines that the printer can then interpret and execute. Slicers can also add supports or adhesion to a part that may be too unstable to print on its own.

Make as many duplicates of the file as colored layers you have. Every time you switch colors, you need a new file. 

Go into your slicer menu and find the layer heights where you need to switch colors. Most slicers insert GCode comments where a new layer starts, so it will make finding a certain layer much easier.

Start with the base layer and find how high it goes before a color swap. Delete everything from the next layer up to the end procedure of the GCode. Rename the file so you know what order to print the files in.

Repeat for all other files, each time going up a layer and deleting everything except for that layer.

Print the files in order from the base to top layer. Between prints, swap out the filament for the color you want for the next layer. Nozzle may require calibration between prints to stay aligned with previous prints.