Preparing a manuscript is not an easy task. Manuscripts are written for submission to journals, with the intent to get them published. While a manuscript for a research paper might be based on a thesis that you have written there are some alterations that will need to be done if you want your work to get approved by publishers. This is because while a thesis or dissertation is meant to be read and evaluated by a review committee that is familiar with your work and the nuances of the subject, a manuscript will have much wider reach. Once published, it will be read by people who may not have in depth understanding of the topic.
The font has to be kept very clear; if there is a font style and size mentioned by the targeted journal, make sure to follow the same. This is important because editors must be able to read the entire text effortlessly. Also, leaving some space for comments by editors and peer reviewers is a good idea. The word count must be kept in check, so that it does not exceed the limit set by the journal editors.

Further, the following points must be remembered while formatting a manuscript:

• Set the margins as per the formatting style that you are following.
• The margin width can vary from 1.5 cm to 2.5 cm.
• Double spacing between words must be used, to enhance the clarity of the text. However, between sentences, use single space.
• Indent each paragraph by ½ inch, or more if so prescribed
• The text should be left aligned as this makes the matter easier to read
• Beginning each section or chapter on a new page is recommended
• There must be a running header on top of each page. It must have the title of the manuscript, and your name if required
• The pagination must be done properly
• All images must be placed as prescribed with the text and labeling must be done in a separate font. Numbering for figures, graphs, tables, etc. must also be accurate so that they can be referred to easily in the text and annexure.
• Create a title page with all the necessary information
• A reference list must be attached with the manuscript with detailed information about all the resources used in the paper

Abiding by the rules for formatting will not just ensure that your editor considers the paper for publication; it will also enhance your chances of getting a fair peer review. So check each aspect of the format minutely before submitting the manuscript.