Update: I also think you really should use an array instead of a hash: @headers.

Good morning,

From what I can tell, you need an array, not a hash:

#!/usr/bin/perl

use Tk;
use strict;
use warnings;

my $mw=new MainWindow;
my @header = ("FHT_neg45","FHT_0","FHT_45","FHT_90","OHT_neg45","OHT_0
+","OHT_45","OHT_90");
my $button = $mw->Button(-text=>"temp",
    -command=> \&button)->pack();
MainLoop;

sub button {
    #Read BJSFM_out.prn into an array @data
    my $filename="BJSFM_out.prn";
    open my $fh, '<', $filename or die "Can't find allowables.txt! $!"
+;
    my $string="Laminate Strain Allowables";

    my @data=<$fh>;
    my $n = 0;    
    for (@data) {
        chomp;
        if ($_ eq $string) {
            $data[$n] = $header[$n];
            $n++;
        }
    }
    open my $write_fh, '<', 'temp.txt' or die $!;
    print $write_fh @data;
    close $write_fh;
}

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I also made a few other changes... three-arg form of open(), lexically scoped most of your vars within the sub (instead of having them global), and changed from using a bareword file handle to a scalar one.

Also, if you have a more current version of Perl, you can change that for loop to using while/each on the array:

    while ( ( my $iter, $elem ) = each @data ){
        if ( $elem eq $string ){
            $data[ $iter ] = $header[ $iter ];
        }
    }
[download]

Update: added in chomp per toolic's point in his above post. I can't test this code as I don't have Tk installed. I've also included the file open check that I missed, as noted by morgon below.

Two further improvements:

First, toolic is right about the need for chomping, so

my @data = map { chomp; $_ } <$fh>;
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and of course check the open:

open my $write_fh, '<', 'temp.txt' or die $!;
 
[download]

I tried to run the following and it replaces $string with %header rather than $string with $header[0], $header1, etc. Also, I thought my print command would add the newlines but it doesn't.

use Tk;
use strict;
use warnings;

my $mw=new MainWindow;
my @header = ("FHT_neg45","FHT_0","FHT_45","FHT_90","OHT_neg45","OHT_0
+","OHT_45","OHT_90");
my $button = $mw->Button(-text=>"temp",
    -command=> \&button)->pack();
MainLoop;

sub button {
    #Read BJSFM_out.prn into an array @data
    my $filename="BJSFM_out.prn";
    open my $fh, '<', $filename or die "Can't find $filename!";
    my $string="1DO YOU WANT INSTRUCTIONS?";
    my @data= map {chomp; $_ } <$fh>;
    my $n=0;
    for (@data) {
        if ($_ eq $string) {
            $data[$n] = $header[$n];
            $n++;
        }
    }
    open my $write_fh, '>', 'temp.txt' or die $!;
    print $write_fh join " ",@data,"\n";
    close $write_fh;
}
[download]

Just an observation. List::MoreUtils has a function apply which does the chomp and passes the modified, (line less the newline), line to @data

my @data= apply {chomp} <$fh>;.

Chris

Update: Or more simply, chomp(my @data = <$fh>);