Working up a tutorial on this for the wiki which when it is done will be at: https://www.shapeoko.com/wiki/index.php/CNC_Finger_Joint_Box (once the wiki comes back up)
First step is to create the box itself: This is done in OpenSCAD using the parameters:
length = 6; width = 3; height = 4; thickness = 0.375; bottomlidthickness=0.125; pins=13; partspacing=2;
Next resolve the pin/joint size and spacing:
Next step is to work out how to get from the above parameters to a file which may be easily cut using Carbide Create — probably using METAPOST.