Mount the emmc in hacdiskmount.
For 100% clean emmc...
Mount SYSTEM, bis key 2.
You will have:
Contents
save
saveMeta (maybe)
1) Delete saveMeta folder if it exists.
2) Go in to save, delete everything apart from 8000000000000120 - you will want to complete initial setup when booted!
3) Go into Contents/placehld. Delete anything that may be in here (probably empty)
4) Go to SD card, delete Nintendo folder. It is now useless.
Unmount, boot. Done.
Not sure if this is correct or not as this info was given by MattyTrog to another user on the forum, but then again
@Sumandora has been known for providing people misleading info, I agree with
@Draxzelex on that.