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.

In reply to Re: Using multiple input files #2 by kennethk
in thread Using multiple input files #2 by ddrew78

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