I am not exactly what the rexec command does but I would think that you will need a | at the end of the open to capture the output of the rexec into your program. Also unless rexec is 8 bit clean and doesn't add any header/trailer information the MD5 sum will not be correct of course. Also, I am assuming the files cannot be made available by some other means (NFS etc).

open(LS, "/bin/ls -l |");
while(<LS>)
{
  print;
}
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This code will print out the ls command output. I think you are trying to do something similar data flow wise.