All of my footnote numbering is not in superscript. How do I change ALL footnotes to use superscript numbers both in text and in footnotes?

To add to what Jay has said, if the Footnote Reference style is correct but your references still aren't superscript, then they may have lost the character style (perhaps because someone selected the entire footnote and used Ctrl+Spacebar (ResetChar) to remove direct font formatting). If that's the case, you'll need to restore it. Luckily, this is fairly easily done as well:

1. Press Ctrl+H to open the Replace dialog.
2. In the "Find what" box, type "^f" (without the quotation marks). This is the code for a footnote reference mark.
3. Click More to expand the Replace dialog.
4. With the insertion point in the (empty) "Replace with" box, click Format, then Style.
5. Select Footnote Reference as the style and click OK. You'll see "Style: Footnote Reference" below the "Replace with" box.
6. Click Replace All.

Note that, if you have text selected when you run the Replace, Word will search only the selected text and then ask if you want to search the remainder of the document. When you do, it will search only the main text layer, and you would then have to search in the footnotes separately. Provided you don't have text selected, Replace All will search the entire document (all layers) and get the footnote references both in the text and in the footnotes themselves.

Word automatically applies a character style named Footnote Reference to both the number in the text and the number in the footnote. By default, that style consists of only the Superscript attribute.

It's possible that the definition of the Footnote Reference style has changed in your template. Do this:

• Select just the number of a footnote, either in the text or in the footnote.
• Press Ctrl+Alt+Shift+S to open the Styles pane on the right.
• Scroll down the list of styles until you find the Footnote Reference (it should have a blue box around it). If you hover the mouse cursor over it, you should see "Font: Effects: Superscript" in the definition popup. If it doesn't say that...
• Right-click the Footnote Reference style and choose Modify from the menu to open a dialog box.
• Click the option near the bottom of the dialog for "New documents based on this template". That will cause the change you'll make to be saved in the template.
• Click the Format button and choose Font from the menu to open another dialog.
• Check the box for Superscript. Leave everything else as is, and click OK in both dialogs.

This should change every footnote number in the whole document at once (assuming they all are formatted with the Footnote Reference style).

After you have done the Find and Replace that Suzanne describes in her reply, make sure that the Footnote Reference style is formatted in superscript. In the Apply Styles pane (Ctrl+Shift+S), type in Footnote Reference. Click the Modify button. In the Modify Style dialog box, click Format, and then click Font. Click the check box next to "Superscript" so that it gets selected. If you see a filled square, click twice so that you see the check mark. Click OK twice.

It doesn't pay to stop reading at the posts marked as Answers when they're 5 years old... The many posts from March 2017 are about a completely different cause of the problem. Reposting Suzanne's post of March 20, 2017:

In several other threads on this topic Michelle V [MSFT] has posted:

• For Office 2016 users who have the Click-to-Run version, this issue is fixed for subscribers in  Version 1702 (Build 7870.2020) or later or for Office 2016 non-subscribers in build 16.0.7870.2020. To get the update immediately, open any Office 2016 app and choose File > Account >Update Options > Update Now.
• For those using volume license editions of Office 2016 who receive updates through Windows Installer technology (MSI), this issue was introduced in KB 3178674 update. Our engineering team is currently working on a fix in an upcoming update. We recommend NOT uninstalling KB 3178674 as this contains numerous improvements and contains a fix for a security vulnerability. We apologize for this inconvenience. We are deeply aware how important it is to resolve this issue and are actively working on releasing a fix as soon as possible. We’ll update this page as soon as we get a fix released.

As commented elsewhere, if you must deliver a document with footnotes before Microsoft gets around to fixing the update, you have little choice except to uninstall KB 3178674 and be very careful about what you do online. And to answer a question that has been asked many times, NO, we don't have any idea when the fix will appear. (Microsoft policy is never to project delivery dates for updates, in case they don't deliver on time.)