Once approach that I can recommend is to open your files inside a scope; once the scope ends, the file handle will automatically be closed. of course, I prefer to explicitly close files handles, but that's just my C background. Something like this:

use autodie;

...

my $config_object;

{
  open ( my $config_fh, '<', 'hello.cfg' );
  while ( <$config_fh> ) {

    .. parse config file ..
    $config_object{ $key } = $something;
  }
}

#  File handle is now out of scope and therefore closed ..
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That's a simple example .. but perhaps you can expand on your question .. why do you think that open file handles are causing you problems?