I've seen a lot of sources from various websites saying more or less the same thing about this issue: that all you need to do is format the card to FAT32 for it to be read by a 3DS. However, I tried that and it didn't work, I was given the "3DS cannot detect SD card" error. So I did a little experimenting and I think I figured out why sometimes it won't work even if it's been formatted correctly.
I opened up the 8GB card that came with my 3DS and viewed the properties in a disk...
How to get an SDXC card (64GB and up) to work with a 3DS
I opened up the 8GB card that came with my 3DS and viewed the properties in a disk...
How to get an SDXC card (64GB and up) to work with a 3DS