C#

private void txtBinNumberInput_KeyDown(object sender, KeyEventArgs e)
{
    if ((e.KeyCode == Keys.Enter) || (e.KeyCode == Keys.Return))
    {
        this.SelectNextControl((Control)sender, true, true, true, true);

FlatFile1:

sampleID ;  rep# ; protein  ; fat ; Lactose ; TS ; SNF ; GLucose;
12334    ;   1   ; 0.23    ;  0.4 ; 0.23    ; 3.4; 4.5 ; 0.9;


FlatFile2:

sampleID ;  rep# ; Water ; TNC ; protein  ; TS ; SNF ; Fat;
12134    ;   1   ; 6.1   ; 2.1 ; 5.6      ; 1.3; 6.5 ; 0.4;


FlatFile3:

sampleID ;  rep# ; Ph ; Fat ; protein  ; TS ;
10986    ;   1   ; 6.1; 2.1 ; 5.6      ; 1.3; 
10207     ;   2   ; 5.0; 1.3 ; 3.1      ; 1.45;  


My Output:
sampleID   rep#   protein  TS   Fat 
12334       1       0.23   3.4  0.4
12134       1        5.6   1.3  0.4
10986       1        5.6   1.3  2.1
10207       2        3.1   1.45 1.3

using System;
using System.Data;
using Microsoft.SqlServer.Dts.Runtime;
using System.Windows.Forms;
using System.Data.SqlClient;
using System.IO;

namespace SSISDYnanic.csproj
{
    [System.AddIn.AddIn("ScriptMain", Version = "1.0", Publisher = "", Description = "")]
    public partial class ScriptMain : Microsoft.SqlServer.Dts.Tasks.ScriptTask.VSTARTScriptObjectModelBase
    {

        #region VSTA generated code
        enum ScriptResults
        {
            Success = Microsoft.SqlServer.Dts.Runtime.DTSExecResult.Success,
            Failure = Microsoft.SqlServer.Dts.Runtime.DTSExecResult.Failure
        };
        #endregion



        public void Main()
        {
            {

                string delimiter = Dts.Variables["User::Delimiter"].Value.ToString();
                string TableName = Dts.Variables["User::TableName"].Value.ToString();
                SqlConnection myADONETConnection = new SqlConnection();
                myADONETConnection = (SqlConnection)
             (Dts.Connections["BIReports"].AcquireConnection(Dts.Transaction) as SqlConnection);


                //Reading file names one by one
                string SourceDirectory = Dts.Variables["User::SourceFolder"].Value.ToString();
                string[] fileEntries = Directory.GetFiles(SourceDirectory);
                foreach (string fileName in fileEntries)
                {

                    // MessageBox.Show(fileName);
                    string columname = "";

                    //Reading first line of each file and assign to variable
                    System.IO.StreamReader file2 = new System.IO.StreamReader(fileName);



                    //Writing Data of File Into Table
                    int counter = 0;
                    string line;

                    System.IO.StreamReader SourceFile =
                    new System.IO.StreamReader(fileName);
                    while ((line = SourceFile.ReadLine()) != null)
                    {

                  if (counter == 0)
                        {
                            columname = line.ToString();
                            columname = columname.substring(length(columname)-1,1).replace(";","")//Not working
                            columname = "" +columname.Replace(delimiter, ",");
                            MessageBox.Show(columname);
                        }

                        else
                        {
                            // MessageBox.Show("Inside ELSE");
                            string query = "Insert into " + TableName +
               "(" + columname + ") VALUES('" + line.Replace(delimiter, "','") + "')";
                            //MessageBox.Show(query.ToString());
                            SqlCommand myCommand1 = new SqlCommand(query, myADONETConnection);
                            myCommand1.ExecuteNonQuery();
                        }

                        counter++;

                    }

                    SourceFile.Close();
                }
                

                Dts.TaskResult = (int)ScriptResults.Success;
            }
        }
    }
}

"Insert into tablename(sampleID ,rep#,Ph,Fat,protein,TS,) values (10986, 1,6.1,2.1,5.6,1.3,)"