National R&D programs play an important role in the development of a country in this age of the knowledge economy. Since many numbers of R&D programs compete for limited resources such as national R&D budget, the R&D program evaluation problem is a challenging decision-making problem faced by decision makers that deal with R&D management. In this sense, DEA(Data Envelopment Analysis) has been regarded as one of the most widely accepted methods to measure the relative efficiency of productivity of R&D programs. DEA is a methodology to measure and to evaluate the relative efficiency of a homogeneous set of decision-making units(DMUs) in a process which uses multiple inputs to produce multiple outputs. However, the sample of the R&D programs could consist of two or more naturally occurring subsets, thus exhibiting clear signs of heterogeneity such as different objectives. In such situations, the fairness of DEA is limited, for the nature of the relative efficiency of a DMU is likely to be influenced by its membership in a particular subset of the sample. In this study, we propose a methodology AI-DEA(attainment index DEA) allowing for reflecting decision maker's subjective judgement on difference among different subsets of R&D programs which have heterogeneous objectives. This methodology combines AHP and Delphi in order to decide the attainmnet index of each DMU for each outputs, and apply them to DEA model. We illustrate the proposed approach with a pilot evaluation of 13 programs involving 6 different subsets of Korean National R&D programs and compares the results of the original DEA model and AI-DEA model.