Recent developments in the area of integrated process and product design have shown that products can be designed in terms of their properties without committing to any specific components a priori. However, the identification of suitable candidate molecules that satisfy a set of property targets is still a challenging issue. While current techniques make use of group contribution methods (GCM) to design molecules, there are many properties which can not be estimated by GCM. Furthermore, not all possible atomic arrangements are represented in GCM. Hence, there is a need of an efficient methodology for the design of molecules that can handle the multitude of non-GCM described properties. In this work, an algorithm is presented that integrates the concept of molecular signatures into the reverse problem formulation framework. A signature is a systematic coding system of atom types. A molecular signature is a linear combination of its atomic signatures. It has been shown that any of the topological indices (TI) of molecules can be represented in terms of molecular signatures and that it is possible to correlate the TI to the actual properties. Using this information, the new algorithm utilizes the property clustering technique in a reverse problem formulation to obtain the molecular structure based on the property requirements estimated in the process design step. The accuracy of this method depends only on two factors: (1) how well the property-TI relationships are estimated and (2) the level of atomic signatures used to describe the TI. Since, many TI can be used to describe each property, this algorithm generally provide reliable results. This contribution will illustrate the developed methods and demonstrate their use in a case study.