Loop over the root directory and for each directory in that folder, start a process, so something like this:
foreach (var dir in Directory.GetDirectories("z:\temp"))
{
ProcessStartInfo psi = new ProcessStartInfo();
psi.Arguments = String.Format("-dir=\"{0}\"", dir);
psi.FileName = @"C:\Path\To\Your\Converter.exe";
Process.Start(psi);
}