It is possible to import your Amazon ebooks directly from the Fire into Calibre. However, since many have DRM (encryption) you are limited in what changes you can make to the these ebooks in Calibre (and they will only work on your Fire).
A better approach, is to import the same ebooks from K4PC or K4Mac. If you use the 3rd party DRM-stripping plugins, the imported MOBIs will be DRM-free and you can customize them however you want. K4PC puts its ebooks in My Documents\My Kindle Content, so import them from there. Note that the plugins have been recently upgraded for the latest K4PC/K4Mac. See Apprentice Alf's Blog for more on DRM.
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