#! /usr/bin/perl

use strict;
use warnings;
use Tie::File;
use File::Copy qw(copy);

my $sourcedir = '/path/to/sourcedir/';
my $targetdir = '/path/to/targetdir/';

my @files = qw(file1 file2 file3);

for my $file(@files){
  copy($sourcedir.$file,$targetdir.$file);
  tie my @array,'Tie::File',$targetdir.$file or die $!;
  @array = grep{$_ !~ /Input/ && $_ !~ /Output/}@array;
  untie @array;
}
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