It is important to remember that the flow of your paper is different from how your project developed. In your research project, you spent a lot time to set up experiments for your project while in a paper those setup experiments are not normally mentioned. When you write a research paper, should not be trying to tell what you have done, instead you want to convey a crystal clear message, which is your finding. This must be the focus of your paper and everything in your paper provides support for that message.
A good method to remain focused on the main message is to prepare an outline. Map out your approach by composing a detailed sentence outline. First, write down a thesis statement, your message. This one sentence statement is the most important one of your entire research paper so be sure to phrase it carefully. A thesis statement clearly communicates the subject of your paper and the approach you are going to take. It is the controlling factor to which all information that follows must relate. Secondly, group and regroup your notes according to the various aspects of your topic until you find a sequence that seems logical. This can serve as the basis for your outline.