We have known for a while that Amiibo functionality was coming to the Nintendo 3DS we just didn't know when, well thanks in turn to the newest Nintendo Direct we now know that Amiibo functionality will be arriving on the 3DS next month. Nintendo has now announced that Super Smash Brothers for Nintendo 3DS will be the first game on the 3DS to receive Amiibo support. It has also been announced that Amiibo will work the same way on the 3DS game as on the Wii U with you being able to take your Amiibo out and about and continue to train them up. Personally I still prefer the console for this but it does give more options to people who have more time on the 3DS game.
As I have stated Amiibo support will arrive next month for Super Smash Brothers for Nintendo 3DS.