The most notable ones are the scar on his left cheek, and the one on his right arm.
The first scar, the one on the cheek seems to have become permanent (although at times, the scar isn't visible in the drawings with negi's face facing forwards; such as in volume cover 21 or 22?)
The second is the scar caused by the "Nagi" illusion created by Albireo Imma (Colonel-san)'s artifact and hence, Negi has allowed the scar to be left untreated since he considers it as a memento of his father.
There is also the scar from having his right arm sliced off by Kagetarou, but it isn't clear yet if it will be permanent since it hasn't been that long.
I think he can use some kind of magic or magical item (like the lotion he used on ch 255) to erase those scars, but he decided to keep the scars as a reminder of those events (it mentioned on ch 255 pg 11 and ch 120 pg 4).
Here are the links:
Ch 255 pg 11 (When he explain why he left his left cheek's scar)
http://www.onemanga.com/Mahou_Sensei_Negima%21/255/11/
Ch 120 pg 4 (When he explain why he left his right arm's scar)
http://www.onemanga.com/Mahou_Sensei_Negima%21/120/04/
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