I think this is what you are asking...
Basically you’re saying you have too many files in the root folder, and you want to re organize it.
Say you are building an extreme sports website (just the first thing that came into my head). And you want to organize your site by sport.
First you would make all the folders (i.e. "surfing", "downhill", "bmxing".) then you would put all the html, asp, php, files that relate to that sport in the relevant folder. (i.e. surfing.html would go in the "surfing" folder.)
Then to link to the surfing.html page from your homepage or any other page for that matter, you would set the hyperlink to
http://domain.com/surfing/surfing.html
But note that your homepage (index.html) must be in the root (index) folder to work.
Hope that helps,
NuGG