Put a unique marker in the file eg <PATTERN> where you want the substitution.

#!/usr/bin/perl
use strict;
use warnings;

my $infile1 = 'file1.txt';
my $infile2 = 'file2.txt';
my $outfile = 'result.txt';

#open IN,'<',$infile1 or die "$infile1 : $!";
#my @file1 = <IN>;
#chomp(@file1);
#close IN;
my @file1 = qw(10000000 00000011 
               10000001 11000000 01100000  );

#open IN,'<',$infile2 or die "$infile2 : $!";
#my @file2 = <IN>;
#close IN;
my @file2 = <DATA>;

open OUT,'>',$outfile or die "$outfile : $!";
for my $pattern (@file1){
  print "Test pattern is $pattern\n";
  for (@file2){
    my $line = $_; # copy to preserve @file2
    $line =~ s/<PATTERN>/$pattern/;
    print OUT $line;
  }
}
close OUT;

__DATA__
SCAN_TEST =

    pattern = 0;
    apply "grp1_load" 0 =
        chain "chain1" = "010";
    end;
    force   "PI" "<PATTERN>" 1;
    measure "PO" "10" 2;
    pulse "/CK" 3;
    apply "grp1_unload" 4 =
        chain "chain1" = "010";
    end;
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