I use the elsarticle document class that Elsevier told me to use. The PDF of my article looks like the sample manuscript on their website:

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But when you look at the journal, all the papers look like this (download the PDF):

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What is going on here? Does the journal do some kind of magic at the end? It is impossible for me to know my figures and everything will align without the correct formatting.

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    One big difference is that articles published in most Elsevier journals use a custom font called Gulliver, which is designed by Gerard Unger. See also Font used in mathematical papers in Elsevier journals. – Mico Jun 17 '16 at 0:46
  • @Mico Ok, but the margins are way different too. Why would they tell you to use elsarticle when is clearly not the final document class? – Forever Mozart Jun 17 '16 at 0:51
  • ok, well in your link it says that the font is proprietary. So this tells me that I cannot make it look like a finished product when I submit. – Forever Mozart Jun 17 '16 at 0:57
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    many publishers provide document classes for authors that do not look like the final published version, but that structure the content so that it can be reliably switched into the "production" style without requiring much manual attention (as long as the author has not made modifications by adding incompatible packages, changing margins, etc.). this decreases the possibility of adding unintentional errors while processing the document for publication. please follow the publisher's instructions in this regard. – barbara beeton Jun 17 '16 at 2:15
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    @ForeverMozart Do not worry too much about the alignment of all the objects. Prior to publication you will be sent a galley proof by the editor asking whether you agree with the placement of figures, etc. If you then feel that something is off the editor will readjust the layout according to your requests. – Henri Menke Jun 17 '16 at 8:43