The optimization optimization problem addressed in this paper is an advanced form of the flexible job shop scheduling problem (FJSP) which also covers process plan flexibility and separable/non-separable sequence dependent setup times in addition to routing flexibility. Upon transforming the problem into an equivalent network problem, two mixed integer goal programming models are formulated. In the first model (Model A) the sequence dependent setup times are non-separable. In the second one (Model B) they are separable. Model B is obtained from Model A with a minor modification. The formulation of the models is described on a small sized numerical example and the solutions are interpreted. Finally, computational results are obtained on test problems. (C) 2011 Elsevier Inc. All rights reserved.