The easiest thing to do is to get Homebrew via Pichaxx and then use Homebrew-only TWLFix below.
To get Homebrew, go over to the Frogminer page and click "I don't have a homebrew entry point", and follow the instructions there.
Once you have Homebrew, come back here and do the Homebrew-only method.
If, for some reason, you can't get Homebrew access, there is a stock-only option. It's a bit more complicated, and requires a DSiWare application from the eShop.
Once you've got a DSiWare application, our good friend MechanicalDragon has written us some instructions here: TWLFix.

What You Need

1. The latest release of TWLFix-3DS (just the .3dsx, NOT the source)
2. Your movable.sed, which you can generate/redownload from bruteforcemovable if you don't have it
3. Access to the Homebrew Menu

Doing It

1. Power off your console and take out the SD card.
2. Put the SD card in a computer.
3. Copy the movable.sed to the root of the SD card. Root means inside SD, but not inside any folders.
4. Copy TWLFix-3DS.3dsx to the "3ds" folder. Note: this means "3ds", NOT "Nintendo 3DS"
5. Safely eject your SD card and put it back in your console.
6. Power on and open the Homebrew Launcher.
7. Run "TWLFix-3DS".
8. Follow the instructions in the application.
9. Once complete, the application should reboot the console.
10. Go to System Settings > Other Settings > System Update.
11. Once the update is complete, your TWL firm should be fixed. Try doing whatever you were previously doing.

What You Need

1. The latest release of TWLFix-CFW (just the .3dsx, NOT the source)

Doing It

1. Power off your console and take out the SD card.
2. Put the SD card in a computer.
3. Copy TWLFix-CFW.3dsx to the "3ds" folder. Note: this means "3ds", NOT "Nintendo 3DS"
4. Safely eject your SD card and put it back in your console.
5. Power on and open the Homebrew Launcher.
6. Run "TWLFix-CFW".
7. Follow the instructions in the application.
8. Once complete, the application should reboot the console.
9. Go to System Settings > Other Settings > System Update.
10. Once the update is complete, your TWL firm should be fixed. Try doing whatever you were previously doing.