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: 
It also depends on what kind of windows application you want to build. If it's just a question of building a simple standalone application then, considering you know both languages equally well, I wouldn't hesitate and would go for a 100% microsoft solution, especially if you have to do specific things like accessing ActiveDirectory, the windows registry, etc.  

Not that you can't do it in Java : you can always use AD through LDAP in Java for example, but the APIs are just "a bit" more complicated than the .Net ones (try to decode objectSIDs in Java without a few tricks). 

Now if you have to build an enterprise app. I just feel that popular frameworks like Spring and Hibernate are always coming out after their Java counterparts (disclaimer : this is a personal opinion; I didn't do any research on this, thoroughly comparing frameworks in both languages, but that's just the feeling I have). I don't know how good the .Net implementations are though, so I don't have a point of view on that. I just remember writing .Net 2.0 apps and not liking ADO.Net at all. 

My view is that the frameworks I like do exist in both languages, but they are first developed for Java, then ported to .Net. 

Now I'm not the kind of developer trying to defend his favourite language over the others. If I don't have external constraints to develop, then I choose whatever language gets my app up and running faster and in the most efficient way.
Yeah for a pure cross platform application Java can't be beat, but if you can manage it Silverlight is a subset of WPF and a pretty compelling cross-platform proposition on its own.

Productivity-wise I think WPF has an edge as it has a nice XAML markup language that can be easily created with the built-in designer in VS.NET or integrates nicely with MS' suite of expression products.