So, what code have you written and how does it fail for your input data?

A good place to start might be something like the following. You will have to modify the regular expression to detect comments and you will have to add other cases you want to detect.

#!perl -w
use strict;

while (<DATA>) {
    s!\s+$!!;
    if( m!\btimescale\b! ) {
        print "Found timescale in [$_]\n";
    } else {
        print "Ignored line [$_]\n";
    };
};

__DATA__
===============================================
// 1st commented line
//second commented line 
// timescale 1ns /5 ns
 
timescale 1ns/4ns  //this comment should also be ignored

module modulename1 (a b c )

some lines.... 
some lines ...


//third commented line 
//fourth commented line 

timescale 3ns/5ns
module modulename2 (p q r)

some lines ...

//fifth comment
//timescale 4ns/5ns

timescale 1ns/3ns 

module modulename3 (m n p )

some line ...

================================================
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For dealing with the comments, I would just wipe out the comment part of each line immediately after reading it. You could do this either using the s/// operator (see the section Regexp Quote-Like Operators in perlop), or using index and substr. The former would be the more "perlish" solution. The latter might look more familiar to you if you come from a language such as C.