Then modifying the Expression in the post we get :
FilteredTable = (From d in dt1.AsEnumerable
Let raf = d.ItemArray.Take(ColumnTake).ToArray
Let chk = dt2.AsEnumerable.Any(Function (d2) d2.ItemArray.Take(ColumnTake).ToArray.SequenceEqual(raf))
Where not chk
Select r =d).CopyToDataTable
Also, to handle the Exception when no rows are filtered we can follow the below :
Note : The assumption is the Headers are not present for the data, hence the Read Range activity Add Headers property are unchecked.