How a thesis is structured is not the same thing as how it is formatted.
STRUCTURE refers to the intellectual arrangement of the thesis. A useful analogy is a cookbook cake recipe. Typically, a cake recipe is structured in the same way.
Cake Recipe Model
A thesis follows a standardized academic structure.
Thesis Model
The End of Program Assessment Manual for Graduate Studies outlines the structure requirements for the thesis/capstone paper.
FORMAT refers to the visual presentation/layout of the thesis, such as margins, line spacing, etc.
Using the cake analogy again. You can use a single recipe to make the same cake, but you can decorate it differently. That is, you can use different styles of decoration.
Academic papers have a required format, or editorial style. The "decoration" or format instructions are found in style guides.
The purpose of a style guide is to provide uniformity in writing and documentation/ citation styles and in formatting a document. Following a standard guide ensures that your paper is professional-looking and readable. Journal publishers typically require authors to follow a specific style guide, so it is a useful skill to know how to use one!
Links to all of the different style guides used in APUS courses on the library's Writing Help Guide: http://apus.libguides.com/writing/citation
For additional information on using style guides successfully, see the Using Style Guides page on this guide.
Learn to distinguish between scholarly and popular articles in this video by Vanderbilt's Peabody Library.