As a suggestion to avoid this kind of problem, if you use a lexical variable as a file handle instead of a bareword, when the variable goes out of scope, Perl will automatically close the file for you. e.g.

open my $file, "<", $filename # use lexical variable

open FILE, "<", $filename # use bareword.
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So if you have a subroutine;

sub foo {
  my ($filename) = @_;
  open my $file,  "<", $filename or die "blah :$!\n";
  while (<$file>) {
    # etc
  }
  # explicit call to close not needed.
}
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The file will be closed at the end of the foo subroutine. If you want the file handle then return it.
And if you aren't using a lot of subroutines but want this behavior, simply start a new block.