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In this paper, an unified approach is proposed to solve forbidden state problems in a general class of controlled Petri nets (CPNs). A new subnet called the step-aligned subnet, which can describe various kinds of PN structures such as marked graphs, state machines and asymmetric nets, is introduced. The step-evaluation method is developed to efficiently investigate the reachable marking problem in step-aligned subnets instead of the full search of reachability graph. The crucial idea of the method is to decompose a large reachable marking problem into a number of smaller subproblems. This paper derives a necessary and sufficient condition in order to find maximally permissive controls in the context of step-aligned subnets. Theoretic results are applied to modeling and control of a flexible assembly cell.