I found a solution for my request.
certreq allows you to issue certificates for a PKCS # 10 request without templates. Templates, including custom templates, can be specified in accordance with Enterprise 2003 CA security policies.
Following is the syntax
certreq -submit -attrib "CertificateTemplate:<Template Name>" <CertificateRequest.req>
Further information on this can be found in MS technet.
thanks
Rajah