1. You could improve readability by assigning those large directory strings to lexical variables.

my $target_dir   = "/data2/jennb/landsat8/antarctica/$dir";
my $download_dir = "/data2/jennb/landsat8/downloads";
[download]

2. I agree with Laurent_R. Look at the POSIX module and try using those commands instead of system("this") and system("that") everywhere. chdir() is a perl built-in, iirc.

3. Consider seeing if your functionality repeats enough to convert some of your code into subroutine/function calls. The for loops with tars and jpegs looks like the first place to start. Long stretches of linear code is a sign that you're not really trying to break the task down by function.

David