A system and method of optimizing a manufacturing process so as to reduce toxic waste in the process. In an embodiment, the method includes: describing the manufacturing process using a plurality of nodes, each node representing a component or a process; connecting the plurality of nodes with directed edges to form a directed graph, the directed graph representing possible manufacturing process flows from a begin node to an end node; assigning to each edge a value representative of a cost resulting from toxic waste generated by a component or process; and determining a shortest path from the begin node to the end node in the directed graph to identify manufacturing process flow having a minimum cost.