Though i know that the normal way, i should have the FI connect to a MDS.
But has anyone successfully configured Cisco 6120 FI to connect to any nexus 5000 series, which is linked up to a storage?
What additional steps should i also perform?
Ensure that NPIV is enabled on the N5K. You'll obviously need to create all the zones & zonesets as you would on an MDS, but the procedure is very similar. The N5K must NOT be in NPV mode.
Are you having any specific difficulties?