You can communicate with the engine using the UCI protocol.
http://wbec-ridderkerk.nl/html/UCIProtocol.html

Some Visual Basic .net code, easy to change to C# to communicate with an engine using STDIN/OUT:

   Private Shared Output As StringBuilder = Nothing
    Dim sortStreamWriter As StreamWriter

Dim process = New Process()
        process.StartInfo.FileName = engine
        process.StartInfo.Arguments = ""
        process.StartInfo.UseShellExecute = False
        process.StartInfo.CreateNoWindow = True
        process.StartInfo.RedirectStandardInput = True
        process.StartInfo.RedirectStandardOutput = True

    Output = New StringBuilder()
        ' Set our event handler to asynchronously read the sort output.
        AddHandler process.OutputDataReceived, _
                   AddressOf SortOutputHandler
  process.Start()

        ' Use a stream writer to synchronously write the sort input.
        sortStreamWriter = process.StandardInput

        ' Start the asynchronous read of the sort output stream.
        process.BeginOutputReadLine()

'send something to engine
sortStreamWriter.WriteLine("position startpos moves " + something)

'read form the engine
Do
            Thread.Sleep(10)
            Try
                Try
                    s2 = Output.ToString
                Catch ex As Exception
                    'sometimes gives an exception
                End Try
                If IsNothing(s2) Then
                    Continue Do
                End If
...

Private Sub SortOutputHandler(sendingProcess As Object, _
         outLine As DataReceivedEventArgs)

        ' Collect the sort command output.
        If Not String.IsNullOrEmpty(outLine.Data) Then

            ' Add the text to the collected output.
            Output.Append(outLine.Data + Environment.NewLine)
        End If
    End Sub