To me, chdir is just Bad (notice the capital 'B').
How about something like

my $tdtRoot = 'c:/tdt/src';
if (opendir (DIR, $tdtRoot))
{
  while (my $fileName = readdir (DIR))
  {
    if ($fileName =~ m/\.tdt$/)
    {
      system ("$BASEDIR/nbsstools/tdtgen/bin/tdtgen $tdtRoot/$fileName
+");
    }
  }
  closedir (DIR);
}
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