%stuff_to_store= (...,...) isn't the way to add something to your hash, it just initializes a hash. Your code will make sure there is always only one hash element in the hash as previous elements are overwritten. Use $stuff_to_store{$dir_to_process}= $file instead.

Note that you are only storing one file per $dir_to_process here. If you want to have a list of files for every directory, you have to upgrade your code to use a hash of arrays for example

while (%stuff_to_store) won't loop through your hash, it will loop as long as anything is stored in the hash and since you don't change the hash in the loop that means forever. Try out print scalar %stuff_to_store; to see what I mean. Use

foreach (keys %stuff_to_store) {
  print $_,'  ',$stuff_to_store{$_},"/n";
}
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to loop through and print out the hash.

"its not working" is the worst problem description you can make. Try to be more specific by telling what your script prints out and what it should print out.