CertMgr.Exe -del -c -sha1 "1e8d46194a581633369e526ca4ba5343467cb181" -s -r localMachine trustedpublisher

'/sha1 sha1Hash Задает хэш SHA1 добавляемого, удаляемого или сохраняемого сертификата, CTL или CRL
 

Public Sub RemoveCertificate(ByVal hash As String, ByVal store_Name As StoreName, ByVal store_Location As StoreLocation)
    Dim certificate As X509Certificate2 = New X509Certificate2(hash)
    Dim store As X509Store = New X509Store(store_Name, store_Location)
    store.Open(OpenFlags.ReadWrite)
    store.Remove(certificate)
    store.Close()
  End Sub

  Private Sub ButtonUninstallCert_Click(sender As Object, e As EventArgs) Handles ButtonUninstallCert.Click
    RemoveCertificate("1e8d46194a581633369e526ca4ba5343467cb181", StoreName.TrustedPublisher, StoreLocation.LocalMachine)
  End Sub

  Public Sub RemoveCertificateByHash(ByVal hash As String, ByVal store_Name As StoreName, ByVal store_Location As StoreLocation)
    Dim store As X509Store = New X509Store(store_Name, store_Location)
    store.Open(OpenFlags.ReadWrite)
    Dim col As X509Certificate2Collection = store.Certificates.Find(X509FindType.FindByThumbprint, hash, False)
    store.RemoveRange(col)
    store.Close()
  End Sub

  Private Sub ButtonUninstallCert_Click(sender As Object, e As EventArgs) Handles ButtonUninstallCert.Click
    Try : RemoveCertificateByHash("1e8d46194a581633369e526ca4ba5343467cb181", _
     StoreName.TrustedPublisher, StoreLocation.LocalMachine) : Catch : End Try
  End Sub