I wanted to trade my 3ds in for a flame red 3ds but I don't know if I can, but I know I still have warrantry left on it so I don't really know anything else.
I don't think Nintendo would change the color of the 3DS for you. I guess you could give them a call at 1-800-255-3700 and see if they would change the color of your 3DS, but I'm pretty sure if they agree (I'm guessing they won't) to change the color of your 3DS, your warranty won't cover it since your 3DS is perfectly fine.
Er, I'm not quite sure what you're asking, but I'll try to respond.
If you mean "Can I contact Nintendo and trade my non-red 3DS for a red 3DS?", the answer would be no. There's simply no service that offers this.
But you are able to trade in your 3DS for a fraction of its value to places like GameStop, and use that towards the purchase of a red 3DS. I would strongly suggest buying the new 3DS first, so you can transfer your stuff over first.
I'm sorry if I sound cynical, I'm in a bit of an odd mood.