Is there a way to copy your DS files from your cartridges and have them as backups on your cpu?

As far as I know you will need a flashcard to use any of the available programs.

If you do have one you might wanna check this one out: https://github.com/AdmiralCurtiss/nds-savegame-manager

Edit: My bad, didn't see this was in 3DS ...

 

TwlSaveTool is what you want. you install it as a cia file. run it with your ds card inserted. It will then ask to create a backup copy of the savefile. It saves. then can be kept safe or used with TWiLightMenu or a pc ds emu if you want. https://github.com/TuxSH/TWLSaveTool/releases

 

Much easier to do it with Godmode9.

Dumping an NDS game cartrige as a .nds file

1. Insert your gamecart into your console
2. Boot your console while holding (START) to launch Godmode9
3. Navigate to [C:] GAMECART
4. Press (A) on the <titleid>.trim.nds file in the drive
5. Select Copy to /gm9/out
6. Press (START) to save and reboot
7. Your dump will be in the /gm9/out folder on the SD card

And your save on the cart will remain on the cart. And the cart will work fine afterwards.

 

Yes pretty much the same way as a ds cart

Dumping a 3DS game cartrige as a .3ds file

1. Insert your gamecart into your console
2. Boot your console while holding (START) to launch Godmode9
3. Navigate to [C:] GAMECART
4. Press (A) on the <titleid>.trim.3ds file in the drive
5. Select Copy to /gm9/out
6. Press (START) to save and reboot
7. Your dump will be in the /gm9/out folder on the SD cart

Dumping a 3DS game cartrige as a .cia file

1. Insert your gamecart into your consoleBoot your console while holding (START) to launch Godmode9
2. Navigate to [C:] GAMECART
3. Press (A) on the <tiitleid>.trim.3ds file in the drive
4. Select NCSD image options...,
5. then select Build CIA from file
6. Press (START) to save and reboot
7. Your dump will be in the /gm9/out folder on the SD card