Question: I am quite aware of both java and C# .Net .when i try to create a new windows application which are the factors that decide which technology should be opted?
I know of one thing ,for great and faster UI development Visual studio helps a lot.

Answer: 
Choose the one with which you are most familiar. The two platforms are different enough that skills from one does not transfer easily to the other.

In any case, try making a trivial application in both your scenarios and see how it works for you. The initial impression is important as it is probably indicative of how well the rest of the work will be.
If its Exclusively for Windows then .Net is best bet.