$sample2 is local to the inner loop but is tested outside the inner loop - it doesn't exist there. use strict would have told you about that unless you have another lexical $sample2 who's scope is global to the for loops.

Generally when you want to perform this sort of matching task in Perl you should first think "hash". Consider:

use strict;
use warnings;

my $file1Data = "1\t2\t3\t4";
my $file2Data = "5\t6\t7\t4";

open my $fileText, '<', \$file1Data;

my @firstLine1 = split /\t/, <$fileText>;
close $fileText;

open my $fileText2, '<', \$file2Data;
my %firstLine2Fields = map {$_ => 1} split /\t/, <$fileText2>;

foreach my $sample1 (@firstLine1) {
    print "Matched $sample1\n" if exists $firstLine2Fields {$sample1};
}
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Prints:

Matched 4
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