In a make-to-order system, orders are scheduled for production based on the agreed due date with customer and the strategy of company. Production planning of such system includes scheduling of orders to the production periods and allocation of workers at different work centers. Complexity in the system arises when the operation to perform next and its processing time is skilled dependent where a higher qualified worker type can substitute a lower qualified one, but not viceversa. Under such working environment, efficient scheduling of orders and allocation of workers at different work center play a major role to improve system performance. This paper develops a mathematical model for make-to-order flow shop system that helps to identify optimum schedule of orders and allocation of workers, under hierarchical workforce environment, with an objective of minimizing the weighted average earliness and tardiness of orders. A heuristic method is also proposed to reduce the complexity and solve the model efficiently.