Flexible manufacturing systems give a manufacturer some capabilities to consider and solve different manufacturing problems simultaneously instead of one by one in a sequential manner. Using those makes her more competitive in the market. One of those capabilities is controllable processing times. By using this capability, the due date requirements of customers can be satisfied much more effectively. Processing times of the jobs in a CNC machine can be easily controlled via machining conditions such that they can be increased or decreased at the expense of tooling cost. In this study, we consider the problem of scheduling a set of jobs by minimizing the sum of total weighted tardiness, tooling and machining costs on a single CNC machine. This problem is NP-hard since the total weighted tardiness problem is NP-hard alone. Moreover, the problem is non-linear because of the nature of the tooling cost. We proposed a DP-based heuristic to solve the problem for a given sequence and designed a local search algorithm that uses it as a base heuristic.