The layout design of multiple-cell automated manufacturing systems includes cell layout design and flow path layout design. Traditional layout methods often treat these two as separate problems and the sequence for solving them is usually cell layout first and flow path layout later. However, approaches of these kinds have one major drawback, that is, they may produce cell layouts that are awkward or difficult for designers to conduct flow path layouts, or cell layouts that do not turn out to be as good as expected after flow path layouts have been performed. Other drawbacks of traditional layout methods include irregular shapes of cells, inaccurate calculations of flow distances, etc. This paper addresses the layout problem of cells and their connecting flow paths in a tree configuration. The proposed layout procedure is designed to avoid the aforementioned drawbacks of traditional layout methods by emphasizing concurrent layout design of cells and flow paths. It combines a search algorithm and mathematical programming models. The search algorithm has a backtracking procedure that allows one to explore alternative layouts, while the mathematical programming models help one obtain accurate layouts of cells and flow paths. The proposed layout procedure also interacts with designers and allows designers to include their qualitative consideration into the layout design. As a result, one can obtain more accurate and good-quality layouts with the proposed layout procedure.