To add the certificate to the trusted root store for the current user programmatically, use the X509Store and X509Certificate2 classes. For example:
string file; // Contains name of certificate file
X509Store store = new X509Store(StoreName.Root, StoreLocation.CurrentUser);
store.Open(OpenFlags.ReadWrite);
store.Add(new X509Certificate2(X509Certificate2.CreateFromCertFile(file)));
store.Close();
See also " How can I install a certificate into the local machine store programmatically using c#? ".
Another option is the Certificate Manager command line (certmgr.exe) tool, specifically:
certmgr /add cert.cer /s Root
where "cert.cer" is your certificate. This imports it into the trusted root store for the current user. However, certmgr.exe is part of Visual Studio and the Windows SDK and may not be freely distributable.