From Nintendo's Support Page
Nintendo wrote:How to Transfer Data Between SD Cards
Step by step instructions on how to transfer data from one SD Card to another SD Card.
Need: Two compatible SD cards or SDHC cards
Need: An SD Card slot on a PC or Mac or a commercially available SD card reader/writer
Do Not: Alter, move, or erase files in the Nintendo 3DS folder.
Do Not: Overwrite data by recopying to the same SD card.
What to do:
1. Insert the SD card with the Nintendo 3DS data into the SD card slot or the SD card reader/writer.
2. Open Windows Explorer (for PC) or Finder (for Mac) and access the SD card.
3. Highlight the data and drag it to the desktop.
4. Eject the first SD card.
5. Insert the second SD card into the slot or reader/writer.
6. Using Windows Explorer or Finder, locate and access the SD card again.
7. Drag the data from the desktop to the second SD card.
Again, from Nintendo's Support Page
: (Games and SD Cards > SD Card Compatibility)
Nintendo wrote:SD Card Compatibility
Information on the types of SD cards that are compatible with the Nintendo 3DS.
Important Note! While it is possible to use SD standard or SDHC standard based cards, we cannot guarantee that products other than a licensed SD card will work.
The Nintendo 3DS is compatible with SD cards up to 2GB in size, and SDHC cards of 4GB and larger.
MiniSD and MicroSD cards are compatible with the use of an SD Card Adapter.