Dear Sunil,
Yes, Employer can file case in civil court not in to criminal,as it is not crime..
but, if you wanted to file case again not serve the notice period by any employee, then i think you should check first the terms & condition of appiontment letter, which given to your employees, as i believ that, most of the companies are putted one clause for short fall notice period, which you must have also added, as like, in case of failure to served the said notice period or any short falls period shall be recover from his salary.
In that case, if his dues are still pending with company then, company can recover from it & then employer can't file any civil case against him. but, if there is nothing any dues are pending or can't be recover from his salary then, you may send him the formal notice of recovery & get it recover, if still he doesnt pay, then you may file the civil case against him.
Regards,
Tushar Swar