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The transparent top is made from a hard coated polycarbonate material (basically a Lexan). If you approach cleaning the top with the care that you approach cleaning the clear coated surface of your paint you'll be off to a good start. I've not had to clean the top other than the occasional dusting with my California duster and of course my car washes. I towel dry the car the same way I do the rest of the car. Don't use aggressive glass cleaners on the top as they can begin to break down the hard coating that it is treated with. It is made to be naturally resistant to scratches.
I am a real big fan of Plexus. This is the plastic cleaner/polish that was developed for canopies on jet aircraft. It is used on most the current high performance aircraft in the US arsenal.
I use it on the clear bra on my car, the headlight lenses, sunglasses, regular glasses and most everything else plastic. In addition to cleaning and polishing it also significantly reduces the static attraction of the plastic. Dust, lint and pollen deposits are significantly reduced.
I have only found it online. It is not sold in stores that I can find.