opendir( DIR, "some_dir" );
@files = grep /[^.]/, readdir( DIR ); # skips "." and ".."
# (assumes you never need to look for files named "...")
foreach $file ( @files ) {
  next unless ( -f $file );
  $outfile = "something_sane";
  open( PIPE, "| $prog1 | $prog2 -x -y | $prog3 > $outfile" );
  open( IN, "<", $file );
  while (<IN>) {
     print PIPE;
  }
  close PIPE;
  close IN;
# and/or unlink or rename that input file so it's less of a bother henceforth
}