Two tricks. If the ASP.NET is to work within sharepoint then create the webapplication within /_layouts directory
If you don't want anything to do with sharepoint, you'll find your sharepoint errors out, so you need to set up an 'excluded managed path' See more in admin help pages.
Go to Sharepoint Central Administration
Configure virtual server settings from the virtual server list page
Choose a virtual server
Choose Define Managed paths
and you can exclude a particular virtual directory (amongst other things) from being managed within sharepoint. Upshot you can create an ASP.NET app that has nothing to do with sharepoint.