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I have one fixed layout epub and I would like to convert this epub in to fixed layout mobi file. What code do I need to remove from epub and what steps do I need to follow.

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This is a very broad question; I'll try to give you some general guidelines, but feel free to post more specific questions if anything in particular comes up while you're doing the conversion.

If you have an epub 3.0 fixed layout file, you should be able to run it through KindleGen and get a working mobi file. The Kindle Publishing Guidelines are pretty comprehensive as well, and should give you plenty of information if there are any particular stumbling blocks. If your fixed layout is a graphic novel, you might want to use the Kindle Comic Creator instead; it offers some interesting functionality specifically for content with panels.

If your epub is one of the old iBooks pre-epub 3.0 files, your first step will be to convert that into an epub 3.0 file and then go from there.

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Since your question is very vague I will try to help and give you some pointers. I would recommend developing for the Kindle instead of trying to convert a fixed layout to a Mobi because you will get a messy output. One thing I dislike about Amazon is their inability to follow along with the industry standards when it comes to fixed layout ebooks. I would advise not using Kindle Comic Creater because it produces invalid code and is based on 2.0 and not 3.0 (that's last I checked on the update of the app several months ago). The GUI is simple enough but if you're going to sell ebooks you should always produce a quality valid product.

Some pointers when building for Amazon:

  • All images should be a background image #page1 { background-image: url("../images/page1.jpg"); }
  • When coding JSON do not multi-line the code it must be all on a single line.
  • Build a dummy sample when using script fonts because most will not render correctly or look terrible on the curves.
  • Always reference Amazon's documentation (Amazon Kindle Publishing Guidelines) the area you will find helpful starts on page 32.
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  • Can you go into more detail about Kindle Comic Creator producing invalid mobi files? This is the first I've heard of it, and we've created some books through it that are currently available without any problems.
    – Tom
    Mar 3, 2015 at 22:06
  • I will have to go back and pull the documents i tested it with. Also, if I recall, it doesnt produce all the metadata fields others rely on even though you're only going to Amazon you should still adhere to a quality standard which Amazon does not
    – DᴀʀᴛʜVᴀᴅᴇʀ
    Mar 4, 2015 at 0:05

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