The employee has no power to hold your original education certificates. The bond paper needs to me read first then only i can quide you the amount payable and consequences. As you have already resigned on [deleted] what is the actual position now? You have paid the amount to the company? is your education certificates are lying with the organization?
If your Manager is not accepting the resignation, do mail your resignation to him and take a print out of the mail.
It will help you in future.