Is modification of the face of a card legal?
Looking at the Yu-Gi-Oh wiki and they have a section on tournament that covers marked cards and it appears to only be concerned about identifying the card without needing to see the front of the card. I have also found some specific topics regarding the penalties for marked cards and a topic just defining what one is.

From what I can see the front is not as important as long as the normal text on the card isn't interfered with (so players know what it does) and the card can't be identified while it is in the deck that marking them on the front should not be an issue.


  A card is considered to be marked if it can be identified without seeing the front of the card. This includes but is not limited to warping, creases, discoloration, card thickness or texture, and water-marks. Ifthe cards are sleeved, this includes but is not limited to sleeves with identifying marks or other unique characteristics that distinguish it from other cards in the Deck. Cards that have been physically altered to add or subtract layers of foil, etc, are not legal for Sanctioned tournament play.


http://yugioh.wikia.com/wiki/Tournament_Rules
http://yugioh.wikia.com/wiki/Marked_Cards
http://yugioh.wikia.com/wiki/Marked_card