Should I file 'Man-Hani' case on my younger brother and his wife on the basis of their letter,which he has sent to my defence office or, first I gave him a legal notice to clear their allegation and then file a case
You can send a notice under laws of defamation in this regard and seek his explanation as well as compensation. After getting a reply you may decide about further proceeding on it.
The audio clip which has proof that how dirty my younger brother's wife abuses my wife , will be valid in court
These are not admissible evidence in court.
May my job is in danger due to such fake dowry/domestic violence allegation because they have not a single valid proof except their oral complain which may take form of written in front of police?
This would not hamper your employment. However it would better that you obtain anticipatory bail.
How can I save my self ,my job and my family from such fake and dirty allegation from my younger brother and his wife side.
Challenge and properly defend yourselves based on the evidences and merits in your side before the trial court.