I had been using my 3DS for about 5 hours today and the battery got low so I shut if off. When I turned it back on to check something 2 hours later the bottom touch screen no longer works. I can still cycle through things with the d-pad/circle pad, but not with stylus or my fingers. Thinking that maybe it had something to do with the battery being low I put it on the charge craddle and it made no differnce. I'm letting it charge fully right now to see if it fixes it, but if the charge cradle made no differnce I'm thinking this isn't going to fix it either. This wil be the second time I've had to send my 3DS in for something (the first being for scratches being caused by the design flaws) if the problem is not resolved. This is pathetic Nintendo. NEVER with any of your other products/systems have I had this many problems with let alone had to have sent things in to get fixed.
In addition to calibrating the touch screen, you should remove any screen protectors in use.
If that does not work, then you will need a repair. Schedule one by calling Nintendo at 1800-255-3700 (6am-7pm, Pacific Time, 7 days a week).
Actually, you can get to the calibration menu without touching the touch screen. First, turn off your system. Hold down L+R+X. While holding these buttons down, press the power button. This should take you to the touch screen calibration menu. (See Nintendo 3DS Operation Manual, Page 15, Below).
I hope that this works for you. Good luck.
Well for whatever bizarre reason, after letting it fully charge over night, now it works. <_<
Huh... I had this same problem and I had to send it in for repairs. When I got it back it didn't work. Then I send it in for repairs again. -_- It didn't work again... But then I put it on the charger. It worked! Let me tell you I was so happy that day.