you can either use Script task in Data Transformation or use T-SQL.
If using T-Sql, load data into temp table with BULK INSERT (all data in one column), then transfer data to another table (Final table) - you need to do some coding in this option.
There is one other option in T-sql, after doing BULK INSERT, you can transfer back data from table to flat file (again BULK INSERT to flat file) , during this transfer, you can write condition to include only data you require and then from there transfer back to Final table (again with BULK INSERT).