Is it possible to make n3ds virgin again? Id prefer to just make it all from the scratch.
Yes, but there would be risks of bricking involved.
Best option is to format the Sysnand with the mSD inserted. This will wipe everything you've done, except for the Mset exploit (So your Sys settings will still be on 4.5).
If you wanted to revert back to complete stock and just say screw cfw all together though, you could use Gateways Menu > Hold UP while selecting the backup option (To restore your Sysnand from the original NAND.BIN you made). *This is what has a chance to brick your system though ***If anything were to go wrong during that process that is.