Some issues with your effort

• the shebang is not an absolute path
• not using strict/warnings, Read this if you want to cut your development time in half!
• you're using <STDIN> instead of @ARGV (as in  perl myprogram.pl)
• you're reading from FILEHANDLE but your printing to STDOUT
• you're using FILEHANDLE instead of $filehandle
• your regular expression is case sensitive and it doesn't match your sample data

The general steps for editing a are

• read from original-file
• modify data
• write to new-file
• rename new-file to original-file

So you might write that as

#!/usr/bin/perl --
use strict; use warnings;
use autodie  2.1001;
use File::Temp qw/ tempfile /;
use File::Copy qw/ move /;
use autodie qw/ move /;
Main( @ARGV );
exit( 0 );
sub Main {
    return Usage() unless @_ ;
    for my $file ( @_) {
        print "Converting $file \n";
        ConvertFile( $file );
    }
}
sub ConvertFile {
    my $infilename = shift;
    my ($outfh, $outfilename) = tempfile();
    open my($infh), '<', $infilename; # autodie dies on error
    while( my $line = <$infh> ){
        chomp $line;
        $line =~ s/sample\_\d\_x?/ID\t/i;
        print $outfh $line, "\n";
    }
    close $infh;
    close $outfh;
    move( $outfilename, $infilename ); #  autodie dies on error
}
sub Usage {
    print <<"__USAGE__";

$0    
$0    modify/this/file 

perl ${\__FILE__}
perl ${\__FILE__}    modify/this/file 


__USAGE__
} ## end sub Usage

__END__
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See use, autodie, open, File::Copy, File::Temp, strict, warnings, perlintro, perlretut, perlrequick, YAPE::Regex::Explain, Beginning Perl (free) Chapter 6: Files and Data, Modern Perl: Chapter 9: Managing Real Programs > Files