There are three main problems that could impact the performance of a Hybrid Manufacturing System (HMS): (1) order release (OR), (2) batch scheduling and (3) worker assignment. This paper deals with these three main problems hierarchically for an HMS. Three different mathematical models are developed to describe the problems more clearly. A novel methodology is proposed to adopt a holistic approach to these problems and find an effective solution. Implementation of the proposed methodology permits integrating batch scheduling and worker timetabling. Feasible solutions in the best-known Pareto front are evaluated as alternative solutions. The goal is to select a preferred solution that satisfies worker constraints, creates effective worker teams in cells, minimizes the number of utility workers, and the average flow time. The study also presents several improvements, which are made following the application of the proposed methodology to a real company that produces expansion joints.