How can I remove sub-folder(controller) name from URL

[eluser]veledrom[/eluser]
[quote author="Aken" date="1331004224"]Why use subfolders in the first place if you don't want the benefit of the URL segment?[/quote]

Because I have massive project to deal with. Wouldn't it be messy having all the controllers under /controllers/ folder? I'm just asking, do you think having separate folders better approach or not? How do I benefit from URL segment in this case though?