It looks like you have introduced a few extra infinite looks while making the code changes. Have a look at the highlighted code below.

I was expecting your rest of the code to remain same except for those single line codes here and there I showed you in the previous post.

Code:
 Dim worker As System.ComponentModel.BackgroundWorker = DirectCast(sender, System.ComponentModel.BackgroundWorker)

        Dim intCount As Integer = 0

        Do While intCount < 1

        Loop

        myProcess = New Process

        Me.Label1.Text = "Run first command"


        Dim sid As String
        ' Start My process coding
        Dim sidIn As System.IO.StreamWriter = myProcess.StandardInput
        Dim sidOut As System.IO.StreamReader = myProcess.StandardOutput
        Dim sidErr As System.IO.StreamReader = myProcess.StandardError

        sidIn.AutoFlush = True

        sidIn.Write("Run First Command" & System.Environment.NewLine)
        sidIn.Write("exit" & System.Environment.NewLine)

        sid = sidOut.ReadToEnd()

        sidIn.Close()
        sidOut.Close()
        sidErr.Close()
        myProcess.Close()

        'Increment intCount by 1
        intCount += 1

        If worker.CancellationPending Then
            e.Cancel = True
            Exit Sub
        End If



        Me.Label1.Text = "Edit the data"


        Dim sourcefile As String = IO.Path.Combine("Path")
        Dim rdrfile As IO.StreamReader = IO.File.OpenText(sourcefile)
        Dim strtemp() As String
        Dim FileLines As New List(Of String)


        Do While rdrfile.Peek <> -1
            If worker.CancellationPending Then Exit Do

            FileLines.Add(rdrfile.ReadLine)
        Loop

        rdrfile.Close()

        Dim writer As IO.StreamWriter = New IO.StreamWriter(sourcefile, False)
        Dim Columns As New List(Of String)


        For Each Str As String In FileLines
            If worker.CancellationPending Then Exit For

            strtemp = Str.Split(" "c)
            If Trim(strtemp(0)) = "FILENO" Then writer.Write(strtemp(11).Trim & vbCrLf)
        Next

        For Each filtereditem As String In Columns
            If worker.CancellationPending Then Exit For
            writer.Write(filtereditem & vbCrLf)

        Next

        writer.Close()
        FileLines.Clear()

        Do While intCount < 1

        Loop

        myProcess = New Process
        ' Start My process coding
        Dim smed As String


        Dim smedIn As System.IO.StreamWriter = myProcess.StandardInput
        Dim smedOut As System.IO.StreamReader = myProcess.StandardOutput
        Dim smedErr As System.IO.StreamReader = myProcess.StandardError

        smedIn.AutoFlush = True
        smedIn.Write("Run Second Command" & System.Environment.NewLine)
        smedIn.Write("exit" & System.Environment.NewLine)

        smed = smedOut.ReadToEnd()

        smedIn.Close()
        smedOut.Close()
        smedErr.Close()
        myProcess.Close()

        'Increment intCount by 1
        intCount += 1

        If worker.CancellationPending Then
            e.Cancel = True
            Exit Sub
        End If

        Do While intCount < 1

        Loop

        Me.Label1.Text = "Run Third Command"

        myProcess = New Process

        Dim sfre As String
        ' Start My process coding
        Dim sfreIn As System.IO.StreamWriter = myProcess.StandardInput
        Dim sfreOut As System.IO.StreamReader = myProcess.StandardOutput
        Dim sfreErr As System.IO.StreamReader = myProcess.StandardError

        sfreIn.AutoFlush = True
        sfreIn.Write("Run Third Command" & System.Environment.NewLine)
        sfreIn.Write("exit" & System.Environment.NewLine)

        sfre = sfreOut.ReadToEnd()

        sfreIn.Close()
        sfreOut.Close()
        sfreErr.Close()
        myProcess.Close()

        'Increment intCount by 1
        intCount += 1

        If worker.CancellationPending Then
            e.Cancel = True
            Exit Sub
        End If

        Do While intCount < 1

        Loop

        Me.Label1.Text = "Run Fourth Command"

        myProcess = New Process

        Dim scl As String

        Dim sclIn As System.IO.StreamWriter = myProcess.StandardInput
        Dim sclOut As System.IO.StreamReader = myProcess.StandardOutput
        Dim sclErr As System.IO.StreamReader = myProcess.StandardError

        sclIn.AutoFlush = True
        sclIn.Write("Run Fourth Command" & System.Environment.NewLine)
        sclIn.Write("exit" & System.Environment.NewLine)

        scl = sclOut.ReadToEnd()

        sclIn.Close()
        sclOut.Close()
        sclErr.Close()
        myProcess.Close()

        'Increment intCount by 1
        intCount += 1

        If worker.CancellationPending Then
            e.Cancel = True
            Exit Sub
        End If

        Me.Label1.Text = "Edit the Data"

        Dim Open As String = IO.Path.Combine("Path")
        Dim Save As String = IO.Path.Combine("Path")

        Dim sb As New System.Text.StringBuilder

        Dim Lines =
            (From line In IO.File.ReadAllLines(Open)
                Where line.Length > 0
        Select line).ToList


        For Each item In Lines
            If worker.CancellationPending Then Exit For

            Dim TempItem = item
            Dim Column1 = TempItem.Substring(0, TempItem.IndexOf(" "))
            TempItem = TempItem.Replace(Column1, "").Trim
            Dim Column2 = TempItem.Substring(0, 20)

            TempItem = TempItem.Replace(Column2, "").Trim

            Dim Parts = System.Text.RegularExpressions.Regex.Replace(TempItem.TrimStart, " {2,}", ",").Replace(" ", ",").Split(","c)

            sb.AppendLine(
                String.Format("{0}{1}",
                              Column1.PadRight(100, " "c),
                              Column2.PadRight(100, " "c), ))


        Next

        IO.File.WriteAllText(Save, sb.ToString)

        Dim inputFile = Regex.Replace(IO.File.ReadAllText(Save), "[ ]{2,}", " ")
        IO.File.WriteAllText(Save, inputFile)


        If worker.CancellationPending Then e.Cancel = True