G'day kshitij,

"I am not able to link the regexp logic to match it based on the output file"

That shouldn't matter as "regexp logic" is not required here. You can do this with Perl's string-handling functions; which are quite likely to be faster than a regex solution (test with Benchmark).

This code:

#!/usr/bin/env perl

use strict;
use warnings;

my $scan_data_found = 0;
my @pins;
my $format = "%-7s %-6s %-7s %s\n";
my @scan_line_data;

printf $format, qw{pattern offset pin_num H/L};

while (<DATA>) {
    chomp;
    next unless length;

    if ($scan_data_found) {
        if (@scan_line_data) {
            my $caret_pos = 0;

            while (1)  {
                $caret_pos = index $_, '^', $caret_pos;
                last if $caret_pos == -1;
                printf $format, @scan_line_data[0,1],
                    join('', map $_->[$caret_pos], @pins),
                    $scan_line_data[2][$caret_pos];
                ++$caret_pos;
            }

            @scan_line_data = ();
        }
        else {
            push @scan_line_data, ((split ' ')[0,1], [split //]);
        }
    }
    else {
        if (0 == index $_, 'pattern') {
            $scan_data_found = 1;
        }
        else {
            push @pins, [split //];
        }
    }
}

__DATA__

                                        p p p p p
Pin Numbers                             3 2 1 8 9
                                        1 2 3 4 5

pattern     offset
scan1        2965                       H L H L H
                                            ^
scan2        2200                       L H H L H
                                          ^
scan3        1100                       H L L L L
                                          ^
scan4        1500                       L L H H H
                                            ^
scan5        2800                       H H L H H
                                          ^     ^
[download]

Produces this output:

pattern offset pin_num H/L
scan1   2965   p13     H
scan2   2200   p22     H
scan3   1100   p22     L
scan4   1500   p13     H
scan5   2800   p22     H
scan5   2800   p95     H
[download]

The split function does take a regex as its first argument; however, that's not the line matching regex you were talking about.