Since Google introduced the new bookmark manager, you can filter the list of folders. To do so, when adding a new bookmark (CTRL+D or clicking the star), choose 'Add to folder' by clicking on the little arrow on the right:
You can now filter the list of your folders. Keep in mind: The filtering unfortunately does not include subfolders (to this day). To find your folder quickly, without having to navigate first, you should keep all your folders on the top level.
The old bookmark manager can't do this and, since it's already been replaced, probably never will.
I tried including screenshots. I'm not allowed because of reputation < 10.