Scenario

There is a server running SharePointPortalServer 2003. It has many web applications running SharePoint sites.  How to remove SharePoint from just one web application?  

Solution

The unextend functionality of stsadm.exe can be used to remove SharePoint from the selected IIS web application

stsadm.exe -o unextendvs -url <url> -deletecontent

http://technet2.microsoft.com/Office/en-us/library/f057d1e5-f8b7-4c92-bb98-3f983df2a2d11033.mspx?mfr=true
http://technet2.microsoft.com/windowsserver/WSS/en/library/c3314243-a583-4e62-a49a-baf706da97401033.mspx

If SharePoint needs to be completely removed from the server, the SharePoint server needs to be un-installed and the other components like indexes, database also need to be removed