Assuming that I was looking at the correct paper, it looks like they are depositing a substrate and the pillars on top, and that's it. Internet disclaimer that I'm not an expert, I don't know how you protect the pillars without having the same dispersive effects that they are fighting. For example, image sensors have glass in front of the sensor (for both protection and low pass), and the pixels are at least an order of magnitude larger, and 100x the area. But, maybe you can just compensate for that as well.
Looks like the pillars are 164nm tall, 610nm high, which is pretty big all things considered. So normal semiconductor cleaning methods are probably fine. But the ways you would clean a camera sensor for instance would be very not fine.