So being the massive Zelda fan I am I decided to purchase the limited edition Zelda 3DS since I did not already own a 3DS. Well I have been using it since Christmas and I am noticing there are small scratches/dot things forming on my top screen. It looks like the raised bottom screen is touching the top screen when it is closed and is causing small dot scratches. I carry it around in my pocket like I did with any other gameboy I have ever owned and I guess a flaw in the design is causing the bottom screen area to scratch the top screen. Can I send it in and get this fixed or not? Because the little dots really kill the 3D when I am playing OoT 3D and I really cannot stand when something I own has scratches on its screen let alone this limited edition Zelda 3DS. I have tried screen protectors but I cannot find any that fit the whole top screen plus it is pretty hard to get them on without having some random piece of lent/bubbles stuck under it. The scratches aren't made by me touching it and I usually do not touch the screen because I know that I might scratch it without a screen protector. Eventually the top screen will have dot scratches all around in the shape of a square... Any help?
The bottom screen's edge touching the top screen is a somewhat common defect, and sending it in for repair won't do anything. You can simply wipe off vertical smudges caused by the bottom screen with a damp cloth. If you are sure that there is an actual scratch in the screen, and it is not just a smudge, then a repair will be necessary.
Here's the thing about a repair. Nintendo usually just repairs your system and then sends it back, which means that you will most likely be getting your limited edition Zelda 3DS back. Sometimes, however, Nintendo will replace the system entirely if enough damage is found. That means that there is a small chance that you will not be getting your limited edition 3DS back. If the scratch is your only issue, though, I wouldn't worry about it.
As for the dots, however, those are not caused by the bottom screen. They are usually just clusters of grime or oil from your surroundings or your hands. Wiping them off with a cloth will work as well.
And you can buy screen protectors that are made for the 3DS. Go to your local game store and ask about them.
You can also buy them online. Here's an example from Amazon: http://www.amazon.com/Nintendo-3DS-Screen-Protector-Kit/dp/B004MKN3VW/ref=sr_1_2?ie=UTF8&qid=1336108528&sr=8-2
Notice that the screen protector kit for the 3DS comes with one larger screen protector for the top screen.