rsriram,

Change @all[$x] which is an array slice into $all[$x]which is a individual element in an array. The below is equivalent to your code.

for my $x (0..$#all)
{
    if($line =~ /$all[$x]/)
    {
        print F2 $line;
    }
}

simply:

foreach (@all)
{
  print F2 $line if $line =~ /$_/;
}
[download]

If you show the input and output, it is easy to help you out.
Also you can do the same using grep and quotemeta.