Seriously, this problem is completely avoidable, and if the 3DS isn't carried around in a way that compresses the top against the bottom, it doesn't even happen at all. When it does happen, it's just finger grease and a little dirt that gets transferred to the top screen from contact with the frame of the bottom screen. That will wipe off with a damp cloth, if it is cleaned promptly. But eventually, if it is not cleaned, and the compressing of the 3DS in a tight pocket of whatever continues, enough abrasive material will accumulate in that gunk to grind in the scratches.
I have gotten the lines on my top screen before, along with 8 little dots corresponding to the ends of the d-pad, and of course the circle from the slide pad. And whenever I've seen these marks, I cleaned my 3DS ASAP. I bought it over a year ago, and it's still spotless-perfect.
I'm sorry, but I can't help but suspect that a lot of people who have this problem are treating their 3DS the same way my 19-yr old son treats cellphones & mp3 players ... somehow they all break within months. I've got a 1st gen Zune that I bought when it launched that still looks and works like new. My AGS-101 GBA-SP is also like new, with not a single scratch on its screen. But I;ve used these 'gadgets' 5 to 6 days a week, for years. My smartphone (a blackberry) needs to be replaced now after 3 years of constant carry and use, not because of any malfunction or breakage, but because it's lame. And as I already explained, my 3DS is also as-new, even though I bought it over a year ago and use it daily.
So, why the difference in gadget longevity of younger people vs. a geezer like me??? If I had to take a guess, I'd day it's because all of my stuff was paid for by ME, with money that had to be budgeted out of a finite amount of income that I earned, which also must pay my mortgage, make car payments, feed and clothe my whole family, maintain my home, maintain our cars, buy Xmas and B-day presents for kids, be put into some savings/investments for retirement, and etc. When all of that is taken into account, even with a nice salary there simply isn't that much room for me to buy toys for myself (I had more money to spend on that kind of stuff when I was 21 than now, and I make about 18 times more a year now than I did then). So, I take care of my shit.
I'm not saying Nintendo isn't somewhat responsible ... streetpass and the inclusion of the pedometer in the 3ds are built-in encouragements from the manufacturer for the consumer to throw the device in a backpack or pocket and take it everywhere he/she goes. But from the very first time I saw those marks show up I knew some extra care was required if I wanted to keep the 3DS like new ... anyone who just ignored this and just decided to wait till it got worse and then send it for warranty coverage caused the problem themselves, through neglect. It's like the complaint is "Hey Nintendo, you designed this thing so it's possible for me to destroy it through neglect. No fair!"
Anyway, that's my old man rant for the day. Take care of your shit.