Hi Pradeep,
We recently solved this problem using Bio-key technology. You basically treat the problem a bit like SAML 2 artifact binding. The website or credential collector forwards you to the specialized website that IDs via the fingerprint service which stores the the userID in a record associated with a random string, a random string is forwarded back in an fcc as if it was the userID, then a custom auth scheme is on the url. This custom auth scheme is some java code that uses a back-channel to talk to the fingerprint service and retrieves the actual userID to disambiguate against the LDAP in SiteMinder.
Hope that made some sense, because it didn't to me the first time.
Cheers,
Ryan