Question: Can a weapon wielded during combat be immediately identified as a masterwork weapon simply by looking at it, or does it require some sort of search, appraise, craft(weaponsmithing) or some other ways to see that it is in fact a masterwork weapon ?

Answer: 
Definitely not. Even with a skill check, it's not plausible to gauge the quality of a weapon just from a glance. The characteristics that make a weapon effective as a weapon (balance, metallurgy, etc. etc.) aren't visible to the eye, or not without close inspection. (Exception: special materials may or may not be easily recognisable.)

If the weapon is distinctive, you *might* be able to make an educated guess: "only the Iron Dwarves make their axe-heads in that shape, and they're famous for the quality of their work". But that would definitely require a skill check (IMHO Appraise or Craft) and you might get fooled if somebody's making cheap knock-offs in the same style.
That's the kind of thing that would be up to the GM. Is this masterwork weapon adorned with jewels that make it appear obviously well made? Does the blade have etchings carved into it? I'd say RAW probably not because it would be difficult to tell the difference between something that was made to look fancy and something that was made Masterfully.