If in IIS you click on the virtual Directory and click convert to application.
Visual Studio will no longer build or publish that virtuqal directory (now applciation).
You do not need to convert your web site project to a web application project, or go through anything more complicated.
Of note: I was having trouble with the CFIDE virtual directory, as this site is also using coldfusion for some other pre-built parts.
Converting CFIDE from a virtual directory to an application has had no affect on Coldfusion, nor any files inside the native CFIDE directory.