There are a few different ways that paragraphs are formatted in MS Word. If you are using APA style, you will need paragraphs that are indented 1/2 inch. Students in CECS also commonly use this paragraph style, but they also sometimes use a block paragraph style with a ragged right justification or a block paragraph style with a right justification. This video demonstrates how to modify the Normal style for each of these paragraph formatting styles.
Also, make sure that you go back through your thesis to correct any text with blue or red squiggly lines below. Correcting some of these problems is also demonstrated in this video.