To export Endnote data to Jabref install the Endnote filter set, which is downloadable from http://jabref.sourceforge.net/plugins/EndNote.zip. Save the “EndNote Import From JabRef” under EndNote\Styles. Then in Endnote go to EDIT-> OUTPUT STYLES -> OPEN STYLE MANAGER and tick ‘Endnote Export’.

To export certain data entries, select them (or all) and go to EDIT-> OUTPUT STYLES ->ENDNOTE EXPORT. In Jabref you can import the file by FILE->IMPORT