If you're asking if there's some way to back up everything all at once, then there isn't. You have to do all the games one by one.
If you're worried about forgetting something, then you can make a backup of the card on your PC. You can always use ninfs to extract save data from a backup like that. In fact, as long as you don't do a complete System Format (which changes the encryption), most games will work fine if you just copy the old save data file back to the appropriate folder.