The process for instrumenting an application is the same, regardless of it being Java or .NET.
You will first need to understand how to application works and what are the critical paths in the application code.
You'll need to start having conversations with your development team to get that understanding.
Then speak with your business analysts about the critical transactions in the application code.
Once you've done the requirements gathering, you'll need to get copies of the application assemblies and use a tool like ILDASM or dotPeek to inspect the assemblies.
Next, you'll need to create a ProbeBuilder Directive (PBD) that instruments the custom classes and methods with your application code. We have a list of best practices and guidance on building PBDs over on APM DEV (http://bit.ly/caapm_dev).
You will next need to add the PBD to your list of directives by 1) adding it to the hotdeploy folder, 2) adding it to the agent profile's directiveFiles property, or 3) add it to an existing ProbeBuilder List (PBL).
To begin testing you'll will need to do an 'iisreset' to restart the managed application.
If you have any further questions about ProbeBuilding, please join us over on APM DEV and ask your questions there. We've setup this subcommunity specifically to help you to extend the capabilities of APM.