You can use map and grep to good effect here:

use strict;
use warnings;

open my $IN, "sample.txt" or die $!;
my $header = <$IN>;
my %sampleID = map { /(.*?)\t/; $1 => 1 } <$IN>; # store desired colum
+ns
close($IN);

open $IN, "sampleValue.txt" or die $!;
$header = <$IN>;
my @samples = split /\t/, $header; 
my @cols = grep { exists $sampleID{$samples[$_]} } 0..$#samples; # sto
+re indices of desired columns

while(<$IN>){
    chomp;
    my @line = (split /\t/)[@cols]; # pick desired columns using array
+ slice
    print join( "\t", @line ), "\n";
}
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