Dear Mr Nitin,
You can file a case under section 138 of N.I Act. Please note that the said provision has been discussed in detail by the Courts and has many provisions which you need to comply with.
You have to present the cheque for clearing and have to send legal notice to the opposite party within 30 days from the date of bouncing of the cheque. The said notice should clearly specify the details of the dispute and it has to be clearly communicated that the in the event the said payment is not cleared within 15 days from the date of receipt of notice you will initiate action under the above stated provision.
If the company fails to clear the dues within the above time, you have to file a criminal complaint in the appropriate court as per the law. That the said complaint has to be accompanied by the pre summoning evidence which would include the original cheque, the memo of the bank stating the reason for bouncing of the said cheque, documents supporting your claim, copy of notice along with the recipt of the postal department.
the Court upon satisfaction will issue summons to the said company. There after summary proceedings would be initiated against the said company.
Wish you luck in your fight.