For information on how to use the Application Signing Tool, see the Application Signing Keys article.
To sign the asp.net web application is the same process, but with some extra steps to follow:
Make sure the target platform matches the IIS Application Pool’s platform (2.0 vs 2.0 or 4.0 vs 4.0)
Under Project Properties -> “Package/Publish Web”, select “All files in this project” option under “Items to deploy”
Disable shadowCopyBinAssemblies in the Web.config:
<system.web> <hostingEnvironment shadowCopyBinAssemblies="false" />