go to https://www.cisco.com/en/US/prod/collateral/optical/ps5724/ps2006/prod_white_paper0900aecd8044aa6d.html
search for "Transport Options for Fibre Channel Extension"
It depends on how much bandwidth you need and how reliable you want it to be.
You could do native FC over Dark Fiber, SONET or DWDM. You'd connect directly to FC port on MDS 9000. You would get a reliable connection with full bandwidth (bw depends on SONET/DWDM cloud)
If you don't need a lot of bandwidth, you could do FCIP. Cisco's MDS supports 1Gbps Ethernet ports for FCIP/iSCSI traffic. You go with MDS 9222i, it has 18 4Gbps FC ports and 4 1Gbps Ethernet ports.
http://www.cisco.com/en/US/prod/collateral/ps4159/ps6409/ps5988/ps8420/product_data_sheet0900aecd8068ec2e.html
Regards,
Roman