There are four approaches to submitting articles to PubMed Central (PMC) - Methods A, B, C, and D. The method selected depends upon the degree to which the article journal/publisher participates in the process.
Each method is outlined using Prezi on this page. A table with an overview of these submission methods is also available on the NIH Public Access Policy website.
Some publishers (called Method D publishers) will submit manuscript files to the NIH Manuscript Submission System (NIHMS) for the author. The author is responsible for the remaining steps in the NIHMS process. This prezi outlines all of these steps.
NIH maintains a list of Method D publishers.
Authors should follow these steps if their journals/publishers will not submit articles directly to PubMed Central (PMC), as in Methods A and B above, and if their publishers submit their manuscripts directly to NIHMS.