Let me repeat what I said earlier - and what has been said many times in other threads: The only time to use the disavow tool is if you have received an "unnatural links" warning from Google - and even then it might have no effect. If you haven't received such a warning, just forget about it.
To answer your other questions:
Many of my client said even after the unnatural links are removed they saw the links in the webmaster tool. I am not able to get this point, even after disavowing, how it is possible, can anyone also experience the same as me.
It takes time for disavowed links to disappear: possibly several weeks or even months.
... is there any size specified for the tool file size that i submit to Google for “Disavow Links”.
No . But it's highly unlikely you'll have many entries in the file. Remember, you can disavow an entire URL in one line. You don't have to disavow each individual link.
Someone suggested me to put comments or reason along with the link, to which i want to disavow. Is this necessary to do this, is there any effect to it, or it is just a formality?
Neither. Comments are for your benefit. They might be useful to you when you are reviewing the list. But Google doesn't look at them, and they have no effect on the disavowel process.