First write to the company /registrar by registered post saying loss of share certificate of FOLIO NO ....... and request for issue of duplicate .
the signature on this request letter should match with the signature with records of company..
the company will ask for many documents like Affidavit ,indemnity bond ,2 surities (guarantors ) with net worth details like balance sheet ,police complaint ,paper advertisement etc etc.
please start the process ....you will come across many hurdles but you have to follow this requirements.if value of share is big company may ask for audited balance sheet of guarantors and even bank guarantee .the process will take more than 6 months or perhaps a year or more depends on how fast you proceed with required documents.
i am doing the process for getting duplicate share certificate of HPCL and Tata elxi hence i might know the latest how the registrar's keep on asking documents .