Nested loops mean that for every line in the outer loop, the inner loop will run once. You're not walking through the two files in parallel, as you see.

Why don't you just read both files into two arrays and iterate over the arrays?

Since your loops are nested, you move through the entirety of file2 before you go to the second line of file1. Perhaps you mean something more like (untested):

print HDLCGET "\#\!\/usr\/local\/bin\/expect\n";
print HDLCGET "set timeout -1\n";

open(MYINPUTFILE, "<", "hdlc2") or die "Open MYINPUTFILE failed: $!";
open(MYINPUTFILE1, "<", "hdlc3") or die "Open MYINPUTFILE1 failed: $!"
+;

while(<MYINPUTFILE>) {
    my($line) = $_;
    chomp($line);
    #my($line1) = <MYINPUTFILE1>; # This slurps the file - oops
    my $line1 = <MYINPUTFILE1>;
    chomp($line1);
    print HDLCGET "spawn \ ssh $line\n";
    print HDLCGET "expect \"assword: \"\n";
    print HDLCGET "send \"$tacacspw\\r\"\n";
    print HDLCGET "expect \"#\"\n";
    print HDLCGET "send \"terminal length 0\\r\"\n";
    print HDLCGET "expect \"#\"\n";
    print HDLCGET "send \"show xconnect all | inc $line1\\r\"\nexpect 
+\"#\"\n";
    print HDLCGET "send \"exit\\r\"\n";
    print HDLCGET "interact\n";
}

close(MYINPUTFILE);
close(MYINPUTFILE1);
[download]

Note also I swapped to the three-argument form of open and added a test to make sure the open succeeded - part of the same advice toolic gave you in Re: using multiple input files. Also, you might read How do I post a question effectively?, as debugging file-processing code w/o the files to be processed can be tricky.

Update: As discussed below, the above code was buggy. Corrected the error and kept the original line as a comment for posterity.

I appreciate the advise. It now moves nicely thru the first file. However, it only reads the first line of the second file, and leaves subsequent fields blank, as shown below. Also, to help out, I added the content of both input files as well.

print HDLCGET "\#\!\/usr\/local\/bin\/expect\n";
print HDLCGET "set timeout -1\n";

open(MYINPUTFILE, "hdlc2") or die "UNABLE TO OPEN FILE hdlc2: $!";
open(MYINPUTFILE1, "hdlc3") or die "UNABLE TO OPEN FILE hdlc3: $!";

while(<MYINPUTFILE>) {
    my($line) = $_;
    chomp($line);
    my($line1) = <MYINPUTFILE1>;
    chomp($line1);
    print HDLCGET "spawn \ ssh $line\n";
    print HDLCGET "expect \"assword: \"\n";
    print HDLCGET "send \"$tacacspw\\r\"\n";
    print HDLCGET "expect \"#\"\n";
    print HDLCGET "send \"terminal length 0\\r\"\n";
    print HDLCGET "expect \"#\"\n";
    print HDLCGET "send \"show xconnect all | inc $line1\\r\"\nexpect 
+\"#\"\n";
    print HDLCGET "send \"exit\\r\"\n";
    print HDLCGET "interact\n";
}

close(MYINPUTFILE);
close(MYINPUTFILE1);
[download]

now gives me the following output:

#!/usr/local/bin/expect
set timeout -1
spawn  ssh 10.247.17.141
expect "assword: "
send "Kalewi13\r"
expect "#"
send "terminal length 0\r"
expect "#"
send "show xconnect all | inc 99999999\r"
expect "#"
send "exit\r"
interact
spawn  ssh 10.247.17.1
expect "assword: "
send "Kalewi13\r"
expect "#"
send "terminal length 0\r"
expect "#"
send "show xconnect all | inc \r"   <-- MISSING LINE 2 INPUT FROM hdlc
+3
expect "#"
send "exit\r"
interact
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here is the content of the two input files. I kept it to three lines for now.

hdlc2

10.247.17.141
10.247.17.1
10.247.17.69
[download]

hdlc3

99999999
616698950
615498584
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Thanks again for the help.

Found the issue, which was my fault. By surrounding $line1 with parentheses in my($line1) = <MYINPUTFILE1>;, we moved to list-context. This means the entire file was being slurped, and the first element of the resulting list (i.e. line 1) was stored to the variable. On the subsequent iterations, the result was undef because the entire file had been read already. Working code:

use warnings;
use strict;

my $tacacspw = 'Kalewi13';

print "\#\!\/usr\/local\/bin\/expect\n";
print "set timeout -1\n";

open(MYINPUTFILE, "<", "hdlc2") or die "UNABLE TO OPEN FILE hdlc2: $!"
+;
open(MYINPUTFILE1, "<", "hdlc3") or die "UNABLE TO OPEN FILE hdlc3: $!
+";

while(<MYINPUTFILE>) {
    my($line) = $_;
    chomp($line);
    my $line1 = <MYINPUTFILE1>;
    chomp($line1);
    print "spawn \ ssh $line\n";
    print "expect \"assword: \"\n";
    print "send \"$tacacspw\\r\"\n";
    print "expect \"#\"\n";
    print "send \"terminal length 0\\r\"\n";
    print "expect \"#\"\n";
    print "send \"show xconnect all | inc $line1\\r\"\nexpect \"#\"\n"
+;
    print "send \"exit\\r\"\n";
    print "interact\n";
}

close(MYINPUTFILE);
close(MYINPUTFILE1);
[download]