I am not sure but I think you can use some color replacement tool in your image editing software?
I sometimes come across with this issue too, especially when I try to download some Internet images for use in my MUGEN characters' big portrait (9000,1 & 9000,2)........
For example, I am trying to mugenize a Cobra character and I searched Internet for some Cobra image for my big portrait (9000,1):
I had to manually remove many unneeded background things and make it transparent, but I also had to deal with the white edge pixel by pixel by hand:
- in case imgur not working for you...:
* this is the end result by using some color replacement tool in my image editing software........the white edge is gone (hopefully) now.........