Hi Maulik,
What might help you is to 'abuse' the Bank Statement option in the Accounting/Bank and Cash menu. Create a new bank statement, give it a name you like and select the corresponding Bank Journal (the one you get the payments on). Use the Import Invoices wizzard and filter for the invoices you want to process and add those to the list. After that press Compute to get the total balance, use that figure to set Starting Balance and Closing Balance of the Bank Statement. Finally press Confirm. All selected invoices will be paid on the date of the Bank Statement, set to done and processed as journal items in the selected bank journal.
Succes!
(PS do not forget to try in a test environment first...)