Model-based Decision Support Systems (DSSs) often use multi-criteria optimization for selecting Pareto-optimal solutions. Such a selection is based on the interactive specification of user preferences. This can be done by a specification of aspiration and reservation levels of criteria. Diverse Graphical User Interfaces (GUIs) can be used for the specification of these levels, as well as for the interpretation of results. In the approach presented in this paper, the specified and aspiration levels are used for the generation of component achievement functions for corresponding criteria, which reflect the degree of satisfaction with given rules of criteria. This paper outlines the methodological background and modular structure of a tool ISAAP (which is included in MCMA) for multi-criteria analysis of decision problems that can be represented as Linear Programming (LP) or Mixed Integer Programming (MIP) problems. The MCMA has been used at IIASA for the analysis of decision problems in water quality management and land use for sustainable development planning. These experiences have shown that the MCMA tool is applicable also to large LP and MIP problems. Other implementations of the same methodology have also been applied to analysis of non-linear problems in several engineering applications.