This paper is an extension of our previous study on pragmatic interoperability assessment for process alignment. In this study, we conduct four case studies in industrial companies and hospitals in order to gather their viewpoints regarding the concerns when condensing process alignment in a collaborative working environment. Used techniques include interview, observation, and documentation. The collected results firstly are summarised into three layers based on our previous developed pragmatic assessment model, and then are transformed into the elements which constitutes the purposed method, and finally based on the summarised results we purpose a method for assessing pragmatic interoperability for process alignment in collaborative working environment. The method contains two parts: one gives all the elements of pragmatic interoperability that should be concerned when considering process alignment in collaborative working environment, and the other one is a supplementary method for dealing with technical concerns.