When compiling, Scrivener 3 applies preset formatting to different categories of folders and documents. It's worth your time to check that your manuscript has the right ones selected.
In any document, go to the Inspector, and click on the tag-shaped icon to bring up the Metadata pane. You'll see a pulldown menu for Section Type. Each project template includes appropriate section types.
The default, "Structure-Based," means Scrivener's taking its best guess about how to categorize this part of your project. You can manually change this by choosing an option below it.
To set a new category for entire groups of files in your documents — i.e., make every folder a Chapter — go to the Edit… option at the bottom of the menu. In the window that appears, choose the Default Types by Structure tab. Here, you can make sure that Scrivener will treat the folders and documents in your project the way you want.
Once you've made sure your files have the right categories, open the Compile box via File > Compile,
opt-cmd-E, or this button in the top button bar:
The options in the Formats column change, depending on what you choose here. Besides print, PDF, or various text and word processing files, you can export to Final Draft or Fountain for screenplays, or ePub or Kindle for ebooks. If you choose the latter, Scrivener will point you to Amazon's site for a free Kindlegen app to create authentic Kindle-ready files.
Each item in the Formats column comes with its own default set of Section Layouts in the middle column.
To pick a new font for your entire book, use the Font pulldown at the top of Section Layouts column. To see different options for how each part of the book will look, click the Assign Section Layouts button at the bottom. Here's where your work in Step 1 pays off.
In the resulting window, you'll see a list of Section Types on the left, and options for how each should look on the right.
Play around with different options until you find the formatting you like best. At the bottom of every list, you'll find As-Is, in case you like your work exactly how you've already formatted it. Click OK when you're done.
The third, catchall column has four panes. First, under the list icon, choose which parts of your manuscript you want to compile.
The "Compile:" pulldown menu lets you compile only what's in a specific folder — handy if, like me, you keep different drafts of a book in their own folders.
The tag icon lets you specify a title, author name, subject, and keywords for your work. The options under the gear icon strip out pesky editing artifacts like footnotes, comments, or annotations. And the ab -> ac icon mass-replaces words and phrases for those last-minute character-name changes.
All set? Hit the Compile button. Scrivener works fairly quickly, so if your finished product doesn't look quite right, go back, tinker, and Compile again until it satisfies you.