sub check_and_insert_into_database {
  my $filename = shift;
  open my $handle,"<",$filename or die "Can't open $filename: $!";
  local $/; # read whole file instead of line-by-line
  my $contents = <$handle>;
  return if ($contents =~ /CLEAR/);
  # insert $contents into database
}
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What have you got at the moment (just the half dozen lines that deal with iterating over files)? It may be that all you have to do is:

    while (...) {
        open INFILE, '<', ...;
        my $buffer = do {local $/; <INFILE>};
        next if $buffer =~ /CLEAR/;
        ...
   } continue {
        close INFILE;
   }
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Prints:

What is the structure of the file? What is the context in which CLEAR can appear? What database are you using?

For Oracle or DB2, and presumably any other database using SQL, you could do all the inserts, and then perform a ROLLBACK if a record containing "CLEAR" is found.