i am in contact with a company having many branches connecting over VPN tunnel and with different IP range in each branch
how can i configure the LMs to discover my switch and my router over VPN
LMS 3.0.1 and higher can use non-CDP discovery methods which should be able to find your remotely connected VPN devices. You could use the Ping Sweep or Route Table modules to accomplish what you want.
See https://supportforums.cisco.com/docs/DOC-9005 for more details.