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HI Sid, To be safe shoot a mail with the picture to the customer care/technical guys. It they respond it would be good and you will have a proof if this is a major issue. One way of checking if this is a surface aberration or surface crack is to get a Dye penetrant test that can be done by material labs guys. If you are in hyderabad I can help you out with this. One other way is to use a fine emery paper and rub on the surface very lightly to see if it disappears. If it does then no worries, but if it is like a crack that is all the way down, you would be in serious trouble if not immediately. The next time you take your bike to service take a printout of the mail that you would send as per my suggestion and have them attest that everything is fine. If there is a problem and you do not get a proper response you can approach the consumer court.

^^ first plz check if it is really a crack by using emery paper rubbing as told above. if it is really a crack, all depends on warranty, if your bike is in warranty, shoot a mail to customer care with photo, tell your service center etc etc... just make sure your bike does not have an accident record (atleast on paper or in insurance else you know it happened because of accident which you did and it is not a fault of company) if warrant y is over, well then buddy... ride as long as you can or change it with your money.

i posted a mail with the picture to customer care they called and asked me to take my bike to service center. In The service center they just opened engine fairings and washed the engine and just examined it visually and conclude that its just on the surface due to improper finishing. But i m still confused as they didn't conduct any test to check it.
AND i have taken 5 years extended warranty and my bike has only done 3200 km on odo.
and my knees on the right side always get black colour prints , i guess something is coming from the engine vents.

from the pic it looks like either a 'deep scratch' or a hair line crack on the outer surface. i would suggest you shoot another mail with the pic after the visit to the svc, and get confirmation in writing from yamaha that 'it is normal and shouldn't cause any damage to the engine/bike or pose a risk to the owner'