I salute all the programmers in the house. I need your help on how to build an application that can analyse data from different sources, identify and remove the duplicates and give the combined and cleansed database as output. I wish to use C# and SQL server 2012.

Knowing the sources you are considering will make helping a bit easy.
Web service?
XML?
...?
...?
Text file?

Thanks for willing to help. The source will be majorly from other DB and excell. Thanks

ADO.net is what you need.
You can connect to database (e.g. MySQL) and datasheets (e.g. excel)
and perform CRUD (Create, Update and Delete) operation on them
I dint debug this, but this code should give you insight on working with excel. Its assumed that you are having an excel file called MyExcel.xls on your drive C

      string conStr = "Provider=Microsoft.Jet.OLEDB.4.0;Data" + 
                              " Source=C:\\MyExcel.xls;Extended Properties=\"Excel 8.0;HDR=Yes;IMEX=1\";";
            OdbcConnection conn = new OdbcConnection(conStr);
            conn.Open();
            OdbcDataAdapter adp = new OdbcDataAdapter("select * from [Sheet1$]", conn);
            DataSet ds = new DataSet();
            adp.Fill(ds);
            dataGridView1.DataSource = ds.Tables[0];
            conn.Close();