Bright saturated noise, sounds like hot pixels ?
MLV app has option to fix bad pixels.
BUT, what helped me a lot to get rid of most of those hot pixels is to do a dead/hot pixel remap in camera.
you can google it, canon pixel remapping.
How it's done.
-Remove lens and put on body cap.
-Turn on camera and to get best results, enable liveview and set it to iso 6400 and leave it that way for a minute or more so the sensor becomes noisy.
-Now do a sensor cleaning in Canon menu (almost in the latest tab of canon menu, 'sensor cleaning' and choose 'clean now'.
After this, you should have much less hot pixels.
Darkframe subtraction is mostly helpful to remove vertical line noise in raw video.
But there is even a better way for 6d.
For low light, you should use LV raw type 0x12 (only works for normal raw recording, not working for high resolution crop module modes)
Not sure if you have a build where you can alter 'LV raw type', it should be available on top in the DEBUG tab of ML menu.
Debug tab -> LV raw type option
Default LV raw type = 0x10
For low light, set it to 0x12, highlight LV raw type option, click set button, use cursor keys to set cursor below the 0 from 10 value, and use scroll wheel on top of DSLR to set it to value 2, so you get 12.
Now use set button to exit and you should have LV raw type value of 0x12
Now shoot a scene in low light, in this mode, even iso 25600 looks great.
Every time the camera is turned off, the LV raw type is set to default 0x10 value.
If you don't have the LV raw type option in DEBUG tab, try the build in this post:
https://www.magiclantern.fm/forum/index.php?topic=25782.msg228784#msg228784