while ( <$fh> ) {
    chomp;           # Remove trailing newlines (a subset of \s)
    s/\s//g;         # Remove ALL whitespace.
    next if /^#/;    # Skip comments.
    next if /^\s*$/; # Skip lines with space, or lines with nothing.
                     # This doesn't make sense because you
                     # already removed all space.  But it
                     # works because you allow it to match
                     # 'nothing' too.
    next if $_ eq "";# This line is never true, because
                     # you already skipped lines with nothing
                     # in the previous statement.
#......