That's already possible, and that's TWO different things.
But "scrubbing" is not the correct word you used for both things you want to do.
1)
Scrubbing is a term used in Wii to replace unused (and random data filled) cluster to allow better compression of the ISO using rar or zip, etc. it does NOT alter the game content, does not extract and does NOT compress the size of the game. the ISO is still 4GB.
There's no need to scrub a 3DS ROM as it does not contains random data after the game data, and already compress the unused part of the file (the one not containing any game information) very well with rar or any other compression format.
If what you want is to get a smaller ROM file, it's not "scrub" that you want but "trim".
Trimming a ROM is possible using
ROM Tool.
It will delete the unused data after the game data. You can save up to 49% of the file size. but only trim CARD1 type games, CARD2 type need some additional sectors after the game data for storing the savegame.
2)
Extracting files is possible, but not with a single program, you also need a console !
ROMs are encrypted, and even if we don't know the encryption key to decrypt the ROM, the 3DS itself knows it (or else it wouldn't play the game) and it will do the job in your stead!
So, you need to do few steps to extract files, and of course you need a hacked 3DS as you will have to run homebrew to decrypt the game on the console.
1- generate a file with the ROM information that will be used by the homebrew (currently only done on computers, with python scripts or with CTRkeygen)
2- run the homebrew with the ROM and that file on the SD card, it will generate a XOR file (not the decrypted ROM)
3- run a program on computer to decrypt the ROM using the generated XOR file and you will get the decrypted ROM.
4- use a program to extract files from the now decrypted ROM.
so, it has a lot of steps, but it can be done.
You can use rxTools to do all the XOR part on the console. I also think rxTool can generate the decrypted ROM directly without generating the XOR file, making one less step needed.
I don't remember all the program's names for file extractors, but other users will help you here
there's probably ctrtool and 3DS Lazy which is also using ctrtool but automate the process.
