There is a really good article out there describing how to write one. Don't have it on me but if you go to the Journal of Hand Surgery website and search around the 'information for authors' section you will find a reference to it.
Paul Manske, Structure and Format of Peer-Reviewed Manuscripts.
You can pubmed it.
It has a few additions specific for JHS (like word-count), but overall it is an excellent primer on how to write an article. Reading past articles is good as well. This thing spells it out for you, though.
An important concept to remember is that scientific papers basically follow the scientific method. You remember this from 8th grade, right? You introduce a problem, give some background information, explicitly state your hypothesis/what you tested, describe your experiment (methods) and its results, then expand on your results and what they mean (discussion), and finally the take-away conclusions and limitations of your study.
As a matter of style you will find that papers don't usually state the problem from the start. Usually they begin with, "Such and such has advanced significantly owing to XYZ. So-and-so discovered QRS which further allowed us to LMNOP. Nevertheless, this one problem remains to be elucidated. Here we did this experiment to see if A>B."
The best advice I can give you is to not fear the blank white page. It is better to write down a bunch of crap and then re-write it several times than to have nothing... because you can't rewrite that.