My started with M so I assumed that it might be with first letter of your Sur/Last name but that might not be true. Certificate registration Number that I receive is after I received my Naturalisation and it consist of Numbers only No Letter.

Try calling their Number 0845 010 5200 and they will find you Reference number or provide you  with proper guidance.  It also says that if you have one.
"1.1 Enter your Immigration and Nationality Directorate reference if you
have one. This usually consists of a letter followed by up to seven
numbers eg S1003752."

As I understand it, IND only starts a file when you have exchanged correspondence with them, so if you have never written to them, and they have never written to you, you may not have a reference. I'd be inclined to leave the space blank, or perhaps just write "not known". They should still be able to pull previous records, using your name and date of birth.
Incidentally, Waheed is correct - the reference is generally the initial of the family name, followed by a long number.

Hi :)

in the application, it said that:

"Immigration and Nationality Directorate reference consists of a letter followed by up to seven numbers eg S1003752. It can be found on any previous correspondence you may have had with the Immigration and Nationality Directore"

Is it also the Certificate of Registration number?  If not, what should i do since i dont have any letter from the IND

Many thanks