Cell formation, scheduling, and facility layout are three main decisions in designing manufacturing cells. In this paper, we address the integration of these decisions in virtual manufacturing cells considering assembly aspects and process routing. We develop a mathematical model to determine the machine cells, the layout of machines and workstations on the shop floor, the processing route of parts, and the production sequence of operations on the machines. In this mathematical model, material handling costs and cycle time are minimized. To the best of our knowledge, this is the first paper that concurrently addresses the scheduling and layout of virtual manufacturing cells with assembly aspects and so-called criteria. To effectively solve the problem, a Population-based Simulated Annealing (PSA) combined with linear programming is proposed. The practical usability of the developed model is demonstrated in a case study. Finally, instances from the literature are solved to evaluate the performance of the PSA. The comparison results showed the superior performance of the PSA in comparison with CPLEX solver and standard simulated annealing.