Простой способ сделать это:
System.Diagnostics.Process proc = new System.Diagnostics.Process();
proc.EnableRaisingEvents = false;
// Set text transform program (this could change according to the Windows version)
proc.StartInfo.FileName = "C:\\Program Files (x86)\\Common Files\\microsoft shared\\TextTemplating\\10.0\\TextTransform.exe";
// Specify T4 template file
proc.StartInfo.Arguments = "C:\template.tt";
proc.Start();