To find the empirical formula, we need to simplify the subscripts in the molecular formula Se₃O₉ by dividing them by their greatest common divisor. The greatest common divisor of 3 and 9 is 3. Dividing both subscripts by 3 gives us Se₁O₃. Therefore, the empirical formula for the molecule with the molecular formula Se₃O₉ is SeO₃.