Dim FileIn1, FileIn2, FileOut As String 'Dateinamen (incl. Pfad) zuweisen!
 
  Try
    Dim data1() As Byte = My.Computer.FileSystem.ReadAllBytes(FileIn1)
    Dim data2() As Byte = My.Computer.FileSystem.ReadAllBytes(FileIn2)
 
    Dim l As Integer = _
    Math.Min(data1.Length, data2.Length) 'Vergleichslänge 
 
    Dim Data_out(l - 1) As Byte
    Dim replacebyte As Byte = CByte(Strings.Asc("#"c))
 
    For i As Integer = 0 To l - 1
       If data1(i) = data2(i) Then
          Data_out(i) = replacebyte
       Else
          Data_out(i) = data1(i)
       End If
       'oder andersherum 
    Next i
 
    My.Computer.FileSystem.WriteAllBytes(FileOut, Data_out, False)
  Catch ex As Exception
    'Fehlermeldung
  End Try