How do I catch application's pop-up message box

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C#

VB

threads

process

automation

, +

Hi,
I have to automate repetitive tasks of a windows application (no API), using VB.Net.
What I did is simulate key strokes usually done by user.
I'm using System.Threading, and initiating the application using a new process.
My PROBLEM is, that this app pops a message box when a task is done, and this message box sure disables the main app window, so I need to know when this message box is displayed to simulate the "ENTER" key stroke and proceed to next task.

Here is a sample of my code:

Imports System.Threading

Public Class Form1
    Dim a As New Process

    Private Sub Form1_Load(sender As System.Object, e As System.EventArgs) Handles MyBase.Load
        a.StartInfo.FileName = "C:\Program Files (x86)\CE\CE.exe"
        a.Start()
        AppActivate(a.Id)

        For i = 1 To CInt(txt.Text)
            DoTask()
        Next
    End Sub

    Private Sub DoTask()
        Thread.Sleep(1000)

        SendKeys.SendWait("^(N)")
        Thread.Sleep(500)
        SendKeys.SendWait("{ENTER}")
        Thread.Sleep(500)
        SendKeys.SendWait("new check")
        Thread.Sleep(500)
        SendKeys.SendWait("{ENTER}")

        Do While True
            'Here I want to wait until a message box pops up by the application
            'If message box displayed then exit do
        Loop

        SendKeys.SendWait("{ENTER}")
    End Sub
End Class

I hope you can help me with this issue,
thanks in advance.