When I started writing my work in Scrivener, I misunderstood the arrangement and didn’t realize separate chapters had to be in separate folders. Now I’ve got lots of individual scenes in one single folder, and I’d like to put each one in its own folder.
Is there any fast way to do that, or am I stuck creating lots of little folders one at a time then moving everything individually into them?
Take a look at Documents > Split; section 15.3.3 in the user manual. There’s a keyboard shortcut.
And you probably want each scene in a text File under a chapter Folder. So maybe convert your chapter Folder to a (text) File before splitting. I think this is the more common way of working but you can go back and forth easily enough.
What chapter folder? I have a story folder with lots of individual scenes in it that are meant to be chapters, so should be in folders of their own.
If I’m understanding correctly you have something like this in your binder:
Manuscript
Story
scene
scene
scene
Where Manuscript may be some other name depending on how you started your project and whether or not you’ve renamed it. Story will have a folder icon (like a paper file folder) and each scene will have text icon (like a page with text on it).
If this is the case you can convert each scene to a Folder (select them all and right click Convert to Folder) and then drag them up a level to the same level as Story and send Story to the Trash.
Alternatively, if your Story folder has a lot of text inside it then you may be able to split it into folders (I’ve not done split on a folder) or if that doesn’t work I think you’ll have to do a Convert to File and split that and then convert all those text Files to Folders.
I suggest a File > Backup > Back Up To… as your next step. This way you’ll have a backup that won’t be automatically overwritten.
The easiest way to grab a bunch of related items and then create stash them into a new folder is to select them in the binder and then use the Documents/Group command. Ungroup, as you might expect, does the opposite (but it will not destroy the folder in case you made a mistake).
But just to be clear, you don’t need to put scenes into folders. That’s certainly one way of working, and most of the templates demonstrate that way of working both in the example binder structures and how the compiler is set up, but you can adapt the compiler to work with nearly any method of organisation in the binder. In your case you might run into an issue with where the chapter break should happen since all of the scenes are in a flat list—but you could easily keep that way of working if that is what you prefer. The software is very flexible about this kind of thing. What I would do is insert a chapter heading file where a page break and title is supposed to appear. Set it to “Page Break Before” in the inspector, and put your title in the document. Then you get to keep everything in one corkboard (which is why I assume you took this route).
But, with this comment, it almost sounds like you are using files called ‘scenes’ that in fact are actually chapters? Why are they called ‘scene’ if that is the case? Perhaps I’m not following what you mean in this statement. If these are whole chapters, then you might want to call them by their chapter names (or if the book itself will not use names and just list “Chapter #” then I suppose you could leave them alone, but surely some sort of naming would make this easier on yourself—I guess that is a personal thing, but personally I’d have a hard time staring at 50 things called ‘scene’ and fathoming the layout of the book’s structure). Then move the files up a level so that they are directly beneath the Draft (or it might be called Manuscript) folder. There is no rule that states chapters have to be folders. In fact files at the top level will act like chapters under the default template compile settings. You will, however need to go into the Separators compile option pane and enable page breaks between files.
I’m not quite sure what the “Story” folder is doing in your structure. Do you have several of them, like parts in a book? If so you might not want to dispense with using the current setup, and rather change the compile Formatting pane settings so that files at Level 2+ look like the way File Level 1 are treated (chapter title and all that).
…don’t need to, rather. 
Did you start with the Short Story template? That would give you a structure such as you’re describing. If each of your chapters is a single document within the “Story” folder, you’re almost certainly going to be better off just switching some compile settings than adding a bunch of folders to contain just one document apiece. That sort of set up, with “Chapter” folders containing “scene” documents, is much more useful when your chapters are broken into multiple documents in the binder, as it provides a convenient way to structure compile rules to output a nice format, but if you don’t break up your work that much then there’s no reason to go to all the hassle after the fact. What you’ll want to do is just adjust the formatting and separators in the File > Compile settings so that you get, say, a page break between each document (i.e. each chapter) and maybe add the document title and a “Chapter N” prefix for the documents. (Note that if your documents are all just titled “Scene” in the binder, then presumably you don’t want to include the title!)
That kind of thing is set up on folders by default in the Novel compile presets, but you can just as easily apply it to the document file type instead–in fact, as Ioa said, this should already be set up for Level 1 documents as well in the Novel compile presets, so if you select all the documents in the binder and just put them directly inside the Draft folder (instead of in the sublevel “Story” folder; in the Short Story template, the Draft folder is renamed “Short Story”), you may not even have much tweaking of compile left to do if you select the Novel Standard Manuscript Format as your compile preset.