...
use Cwd qw(abs_path);    ## module to get absolute pathname
  ...
  foreach my $my_file(@lines){
     $my_file = abs_path($my_file);  # get the absolute pathname of each file
     open my $fh2,'<',$my_file or die "can't open file: $!";
        while(<$fh2>){
         ...
        }
  }
 ...