Transferring software between the System Memory and an SD Card
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Downloaded Nintendo 3DS download software and Virtual Console titles will be saved on your SD Card, while downloaded Nintendo DSiWare will be saved on the System Memory.
Only Nintendo DSiWare can be moved to an SD Card and back, but it's not possible to launch a Nintendo DSiWare title from the SD Card itself. To move a Nintendo DSiWare title/s, access the System Settings option of your Nintendo 3DS system and select Data Management. Tap the Nintendo DSiWare icon and follow the instructions on the screen.
Please note that it is not possible to launch software saved on an SD Card on another Nintendo 3DS system. It can only be launched on the Nintendo 3DS system from which you saved the software.