Might I suggest you look into D-25 nippers, they are commonly considered the best on the market behind God hands: http://www.amazon.com/Nipper-Thin-Blade-Premium-D-25/dp/B00318PWL0
That sandpaper is perfect, just be gentle with the rougher grits and work your way up, I personally go: metal file, 1200, 1500, 2000, but you may find you prefer a different pattern (file not required, purely my preference), so try different combinations and you'll find why works best for you.
And as for the hobby knife previously suggested, I don't use one for nub removal (do have one though), some people prefer a knife, I just feel sandpaper gives a better finish with less chance of gouging the plastic or you lol, but do feel free to try one.
Hope that helps, good luck :D
You don't have to get God Hand nippers - but once you try them you won't want to use anything else.
Nub marks are a bane. Some fine sanding paper or even nail buffers from the dollar store can really help after you trim with an exacto.
The thin blade tamiya are a nice balance if dropping $40 on Godhands is out:
https://www.amazon.com/gp/product/B00318PWL0/ref=oh_aui_search_detailpage?ie=UTF8&psc=1
And BTW, I like how you posed it in front of the box. :)
I have those. I used them for a few years, but just switched back to side cut nippers. For thicker nubs they take a lot more force to cut and it can be difficult to get at some parts due to interference from other parts and the need to be at rightish angle to the part you are cutting. I would recommend a good side cutter (god hand nippers). I now use D-25 nippers: http://www.amazon.com/gp/product/B00318PWL0/ref=oh_aui_detailpage_o06_s00?ie=UTF8&psc=1