3ds Black Dot issue

The black part on the green-haired girl's head? Looks like a broken LCD. I don't think there is anything that can be done to fix it. So…
…Consider replacing the upper screen but be warned: replacing anything in the upper screen assembly is not an easy thing. If you're not used to this you might easily break the console further. Refer to ifixit.com for instructions.
Professional repair is pretty expensive while the part (LCD) is affordable.

Good luck and have fun!

 

Well, I fixed a similar problem with my console on an akward/tedious way, if you will, but it had not good consequences after all (I remove the black stain of course, but the screen now has a permanent burn effect and sometimes retroilumination fails).

Just for your information you can check this link narrating the facts (is in spanish, but I believe you can use the web translator to read it, if you will).

 

If you're going to change the screen,

• Help yourself and buy both the LCD screen and the plastic screen protector with the adhesives
• Use 2 pins to remove the 4 rubber pads in order not to mess them up. (heat up the top screen to melt adhesive, slide one straight down and lift a bit, then slide the second one under the plastic foil and only then try to lift everything)
• Have a look at multiple tutorials available to prepare yourself for the flex cables pass through challenge

Might be worth trying fmkid's idea first...

• Heat up the top screen
• use a succion cup to remove the protection without damage
• rub the screen with the stylus (don't know too much about this, refer to fmkid's link)
• cleanup and stick the screen protection

 

Yeah, that's basically what I did . But, anyway, I don't recommend it (only if you are impatient or if you don't have enough money or knowledge to change the entire screen, but at your own risk), because I got (nasty) colateral effects after all .

PS: I also used some available .3dsx apps to clean/fix dead pixels (one made by master @zoogie, afaik), after rub the screen, to get rid of certain remaining black dots. It took several hours and tries, I have to say it too

 

@rolenks, if you're not comfortable replacing the upper LCD yourself,

• [iFixit] New 3DS XL Repair
• [eBay] Replacement Upper Top LCD Screen Display for New Nintendo 3DS XL 2015
• [ZedLabz] Top LCD screen for New 3DS XL 2015 Nintendo OEM upper display replacement - PULLED

have one of these repair specialists fix it for you,

• wiigotem - [eBay] 2015 Nintendo New 3DS XL Game System Repair Service,Hinge,Slot,Charger Port&More
• testerfan - [eBay] Fix Broken AS IS Nintendo New 3DS XL 2015 Model System Parts and Repair Service!