I would like to un-publish binaries (PDFs) which are not being referenced in any of the component currently. How can I achieve that? please help
The reason why you specify a "Related Component" when adding Binaries in the CM API is so the Binaries can be unpublished (indirectly, by unpublishing that related Component).
RenderedItem.AddBinary overload which does not take a
relatedComponent parameter is marked as obsolete with the following warning:
Adding binary data without specifying a related Component results in unmanaged binaries in Content Delivery. Use an overload which accepts a relatedComponent parameter.
So: AFAIK, there is no (supported) way to unpublish Binaries which were published without specifying a related Component.
If I understand correctly you looking for static binary assets to be published to FS, those binary assets not been used in any component or pages metadata. if it's yes then it's possible.
refer to @Nickoli Roussakov's article nicely explained with sample code. http://www.tridiondeveloper.com/publish-an-image-to-a-structure-group-mirroring-folder
I hope it helps.