You can easily do what you suggest. Aperture arranged the library based on the file structure you imported from a series of folders on your HD at some point.
The structure is very flexible in a Managed Library.

Before you start, you need to be clear on the role of Folders, Projects and Albums.
In a Managed library structure:
Projects contain your master files and edited versions of those masters.
Albums are sub categories of versions of your Master files from a Project or from multiple Projects. They are not additional copies of Master files.
Your Master Files remain in the Project unless you drag the original out to anther project
A Version of an photo can exist in as many albums as you like with out effecting the size of your library (OK a little bit but its not a copy of your master).

Folders contain only Projects and Albums. You cannot drag and individual image into a folder.
To reorganize your library the way you want
You can simply drag your Projects and Albums out of your folders.
When your folder is empty you can delete it from the library structure by selecting it and clicking Aperture/File/Delete Folder.
Hope that helps

Soheil,

Let me restate what you are asking and if I’m right, I think I have your solution.

You had this ugly file structure of images on your hard drive to start with. You imported the whole thing into Aperture as a referenced library and Aperture retained that structure within it’s library.

Let’s make sure you did the import as a referenced library first. When you did the import, did you set the “Store Files:” popup menu to “In their current location”? If you did you do have a referenced library and Aperture is attached to those original files. If instead you had it set to “In the Aperture Library”, then Aperture actually copied all the images inside its library file and is no longer caring about those originals.

If you really have a referenced library, then the Relocate Originals… command in the File menu can do what you want. Once you’ve organized all your images in Aperture, select the Photos view in the Library pane and select all images in the browser window. Then choose File->Relocate Originals…

In the resulting dialog you can control how Aperture organizes the images. There are several presets you can use and you can use the edit menu to create your own. At the same time Aperture will rename the image files based on the naming preset chosen.

I suggest taking a look at it and do a trial relocate with just a few images to make sure it is doing what you want.