Running an ASP.NET application on a server with a SharePoint instance requires excluding the virtual paths the application needs, as the SharePoint ISAPI filter will intercept all requests. This post assumes you have SharePoint installed as a Default Web Site.
1. From the Administration Tools, click on SharePoint Central Administration.
2. Click on SharePoint Portal Server in the left menu.
3. Click on Configure virtual server settings from the Virtual Server List page.
4. Click on Default Web Site.
5. Click on Define managed paths.
6. Enter a path, check Exclude Path, and click OK.