While publishing a unstructured framemaker document to pdf, the Header and footer is getting in the final published document. Please provide a solution.
Perhaps the headers and footers are outside the page size when viewing the master pages? Or your master pages are not applied correctly?
I would do what Bowen suggested and perhaps look into your master page usage: Format > Page Layout > Master Page Usage.
If you added new master pages to the document, it's possible that they aren't being applied correctly or you inadvertently didn't add content to the master page being applied.
What Master Pages are assigned on the pages that work, and the pages that render without Header & Footer?
Format > Page Layout > Master Page Usage
If not "Left" and "Right" for all, then either:
Does the document have a Reference Page named "MasterPageMaps" containing an "UnstructMasterPageMaps" table? (It won't until the first time Apply Master Pages is requested).
There are myriad other possibilities as well.