I Need to use the Ejbca for my .net application.How we can use it for .Net.
First of all EJBCA works for .net or not.
First of all, EJBCA is a certification authority based on enterprise java beans and as a such is based on java technology.
You can integrate EJBCA services with your .NET application of course. Certification authority and its functions is independent of where you want to use certificates.
You should provide more details about what you want to achieve to get a better answer.