Getting dynamically the directory and files under that directory.

What is logic for to get the date folder name ? Is it current date/yester day's date ?

Otherwise, you arrange the folders based on the name descending order. So, you'll get the latest folder name always in the top.
Then pick the Top 1 folder name and you can use your code.

string LatestFoldername = GetLatestFoldername("E:\Data\CommercialEOB\MRDF\")
List<string> fileList = new List<string>();
            DirectoryInfo di = new DirectoryInfo(@"E:\Data\CommercialEOB\MRDF\" + LatestFoldername);
                        FileInfo[] fi = di.GetFiles("*.txt");
            if (fi.Length != 0)
            {
               foreach (FileInfo file in fi)
               {
                  Console.WriteLine(file);
                  mc.MRDF = file.ToString();
                  mc.logPath = @"C:\temp";
                  mc.Run();
               }
            }
            else
            {
               throw new Exception("No File Exists ", new Exception());
            }
         }


private string GetLatestFoldername(string path)
{
        1) Here you get all the sub-folders of the specified directory (path parameter)
        2) Sort the folder names based on the name / folder created date time decending order.
        3) Pick up the top 1 folder name and return that top 1 folder name.

}

Hope this helps you.