I'm wondering what my options are in this specific scenario while using Winhost. My issue that I ran into on my test server is that I have the following website structure Application A Root - folder - folder - Virtual Application B Root (MVC application that resides in subdirectory of Application A) I am deploying my applications through MSBUILD with /PeployTarget=MSDeployPublish parameter to use Web Deploy. Everything worked fine until I added the Virtual Application in the subfolder under Application A. When I went to deploy Application A, it tried to delete the Virtual Application B folder and couldn't because it was being used by another process. That makes sense. So there were two ways I can get around this. I can add the /P:SkipExtraFilesOnServer=true parameter so that it doesn't try to delete anything when it deploys. This works, but I want my directories cleaned up so that extraneous files are not left out there. My next option is actually create my Virtual Application but point the source to a location outside the actual Application A Root. So my structure would look more like this then. Application A Root - folder - folder - Virtual Application B (points to Application B root) Application B Root This works when I full control in IIS but I'm not sure if this will work while using Winhost. Is it possible using Winhost to set this up? Right now my Application A sites in the root of my site so I cannot move my Application B outside of the Application A root. I could make my Application A root a subfolder under my site, but then the url to my main site will like www.mysite.com/applicationAsubfolder which I absolutely do not want. What are my options here?