Is there a way I can use the sharepoint controls in a ASP.NET web application like any other controls that come out of box for ASP.NET? If yes, what are the pre-requisites I
What specific controls are you referring to? Those that you find in SharePoint Designer?
If you are referring to Web Parts in WSS v3, those that are using the ASP.NET Web Part as the base web part (the recommended approach) may work fine in ASP.NET since the Web Part class inherits from Panel which inherits from Web Control (going from memory here) - all ASP.Net classes. It would just depend on whether the web part has any SharePoint specific code which is highly dependent upon the web part.