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: 
There are several factors I would consider...

What are your programmers used to working with already? What third party libraries are you likely to need, what's available on both platforms?

Does platform independence matter to you?

Would LinQ be advantageous?

If you're starting from scratch, costs for the platforms?

Both platforms have strong communities around them...

Hope this helps...
...But with java you will have crossplatform application on scratch.
Also coding UI in java is not difficult - if you read some guides before and use some frameworks as swing application framework or SWT framework.