According to the answer provided by REMESQ on this question: Is it possible to use razor layouts with Orchard CMS and bypass the theming I was able to have separate layout and pages for a module bypassing Orchard's themes and layouts. But having problem referencing the cs,js script files (located in different folders of the module). Getting 404 NotFound error.
I tried referancing in the following way: @Script.Include("~/Scripts/jquery-1.9.1.js")
But cant get the correct reference path rendered attached picture