Although Functional Size Measurement (FSM) methods have gone a long way, they still provide challenges for software managers. A major challenge is related to the comparison of the well established FSM methods. This paper identifies the conceptual similarities and differences among MkII FPA, COSMIC FFP and IFPUG FPA methods based on a case study, which involves implementation of the methods to measure the functional size of a military inventory management project integrated with a document management system.