The process to format an SD card to FAT32 is different for each operating system.
Choose your operating system
Optionally, if you have a 3DS with custom firmware, you can instead use GodMode9:
If you do not need a guide for the above SD formatter tools, here are direct links to their pages:
- Windows: SD Association Formatter + guiformat
- Mac: Disk Utility
- Linux: GParted + [dosfstools