To create a .bib file that only includes the citations you used in the manuscript:
bibexport -o extracted_file.bib manuscript.aux
There are a few issues with this though. The command bibexport comes with the installation of TexLive, but my Windows computer (bless) does not cooperate (“bibexport is not recognised as an internal or external command…”) . So I can only use it on my Mac (luv ya).