This is from some old note I dug up, but should work:
Process proc = new Process();
proc.StartInfo.FileName = @"C:\Program Files\Ipswitch\WS_FTP Professional\ftpscrpt.com";
proc.StartInfo.Arguments = @"-f P:\share\getfiles.scp";
proc.StartInfo.RedirectStandardOutput = true;
proc.StartInfo.RedirectStandardError = true;
proc.StartInfo.UseShellExecute = false;
// start the process
proc.Start();
// wait for it to finish
proc.WaitForExit(5000);
// get results
string output = proc.StandardOutput.ReadToEnd();
string error = proc.StandardError.ReadToEnd();