Property dispute

First of all your father is wrong in constructing in addition without any sort of agreement with your uncle. If your uncle has not contributed any funds for the additional construction and remained silent for the same without objecting, then he is bound by the doctrine of acquiesence. He cannot claim any right over the additional construction made by your father. But you have to file a civil suit before the competent civil court having territorial jurisdiction for declaring your father's right over the aditional construction and seeking injunction against your uncle from using the same or ernting out the same. You must have very strong documentary evidence to prove that the additional construction was done only with your father's money and your uncle made no contribution to ti at all. Then only you can succeed.

My father had a stamp paper where my uncle had written that he has no objection with additional construction and will not claim on the newly constructed area. Will that work??

Yes. this stamp paper is enough for documentary evidence in the court of law.