It depends... Champions is an Effects based system. That means that if what you are describing has an effect it has an associated cost or point break in the form of a complication. I am less familiure with the 6th edition than the others but from what I understand this should all be easier in 6th.
For the Scar it could be something as simple and cosmetic as it makes you recognizable and has no other effect, in that case take the distinctive features complication and that is it. If you want the scar running through the eye and making him blind on that side then it would give a bunch more points and be written up as a Physical Limitation.
As for the metal laced bones and whatever other serum enhancements your super soldier got... you don't pay for metal laced bones you pay for whatever bonuses they give you and justify and describe them as metal laced bones or super-soldier enhancements. I would probably build it as a relatively low power elemental control and lump some always on density control with more Str, Con, PD or damage resistance along with maybe a minor boost to normal HtH damage. I don't know for sure about 6th edition but almost all the editions of Hero/Champions have had a martial arts style called Commando Training or some such that would apply, if your guys is a specialist you might want to go with more than one style and get full fledged Boxing, Karate or Savate and then some softer style like Judo, Aikido or Wrestling.
Really you can build this guy however you want. That is the beauty of Champions. But remember you pay points for raw mechanical effects and the visuals and story bits that justify and describe what those effects are is pure color.