If your script is taking quite a while to run, its probably a loop or two thats doing most of the work. So, somewhere in your loop, just have your program output a "." every once in a while:

use constant PROGRESS_CHUNK_SIZE => 1000;
my $counter = 0;
while ( ... ) {
   # loop that takes a long time to run
   ...
   $counter++;
   if ( !($counter % PROGRESS_CHUNK_SIZE) ) {
       print ".";
   }
}
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You may want to alter the PROGRESS_CHUNK_SIZE value, depending on how long 1 loop iteration takes.