My question is, why do you want to do this?
If it's purely organisational then your "simple folders" should really be enough, so maybe you need to re-think your project structure.
If it is for compilation purposes, like it takes ages to recompile the site every time you change something, maybe you could split the site into multiple site project that each run as a subdomain of your main site.
These will then be recompiled separately.
If it's an organisational thing but related to management, in that you have loads of code and it's difficult to get around then maybe you should assess the way you are building the site. Would an N-Tier aproach or ASP.NET MVC provide better separation of your code?
What do you think?...