I have a window contains 3 columns and 60 rows
I assume you mean you added a JTable to a window.
I modified something in my pop-up window. But before i save it, i come to parent window and intentionally/unintentionally sorted a particular column.
If I understand the question then your "pop-up" should be a modal JDialog. That way you won't be able to click on the parent JFrame until the dialog is closed.