A crucial step in the logic-control design for flexible manufacturing systems is the modeling of the desired behavior in terms of production sequences. These are typically expressed as a series of informal specifications which are to be translated into a formal model. The present paper introduces a Petri net-based methodology for the modeling of production sequences conceived as an incremental process, which progressively adds subnets to a partial model until all specifications have been included. A formal verification of the model is performed at every stage, so that specifications, which are incongruent with the current model and can jeopardize its correctness, can be detected and rejected or modified. No unnecessary modeling constraints are imposed on the model class and behaviors characterized by complex alternative-parallel relationships between operations can be represented. A specific algorithm is provided for the automatic synthesis of complex connection structures in the model, allowing for greater flexibility and complexity in the design process. Note to practitioners - Petri-net (PN) models can be effectively used in the development and validation of industrial logic-control systems as long as well-structured modeling techniques are available that can be easily automated in a computer-aided design environment. This paper introduces a structured and modular novel design methodology based on PNs, which constructs the logic-control model in an incremental fashion, taking progressively into account the user's product-flow specifications, in terms of composition constraints on the operation execution. Each step of the design process increases the model according to rules which guarantee that it holds specific well-definiteness properties. In particular, the methodology prevents possible design mistakes from leading to deadlocks. From a practical point of view, the design process fits the step-by-step specification method that is commonly adopted quite well, w- ith the great advantage of having immediate feedback on the formal correctness of the model at each step. Also, given a suitable implementation in software packages, the interaction with the user does not require specific knowledge of PNs. The actual control logic can then be obtained by adding the resource model to the product-flow model and detailing operations.