The picture on the left is a screenshot of the model in the Fusion 360 (the software to design it). In Fusion 360, we can decide where to have a hole and anything you want to have on the layer. And we can output the stl file in Fusion 360. Afterwards, we may open the stl file in Cura or other software which creates the Gcode. The 3D printer can read the Gcode and finally print the layer.
All the files can be downloaded at //www.thingiverse.com/thing:2484275