Hi Imran,
In addition to Junaid Wahab's great advice if you are starting with a clean *nix MOM installation before you start the MOM for the first time you can just zip up the Windows SmartStor (/data directory) and copy it to the same location on your *nix MOM.
Binary copy of a Windows SmartStor to a *nix SmartStor is valid.
NOTE: I forgot to add that before you zip up the Windows SmartStor (/data directory) you need to stop the Windows EM.
Regards,
Lynn