A three-dimensional inverse design problem is examined in this work using a general purpose commercial code CFD-ACE+ and the Levenberg-Marquardt Method (LMM) to estimate the optimal perforation diameters of perforated pin fin array based on the desired temperature difference between base plate averaged temperature and ambient temperature (triangle T) and system pressure drop (triangle P). The analysis consists of three cases. In design #1, five design variables are used to estimate the optimal perforation diameters and the objective is to minimize triangle T and triangle P of the pin fin array. In design #2, four design variables are considered to determine the optimal perforation diameters based on the minimization of triangle T and triangle P. In design #3, all the perforation diameters are assumed identical and use only one parameter to determine the optimal perforation diameter based on the minimization of triangle T and triangle P. The numerical design results show that, for all six designs considered here, the designed optimum heat sinks always have the lowest average base plate temperature, it can decrease from 6.3% to 7.3% when compared with the solid pin fin array. Finally, experimental verifications are performed on these heat sink modules and the results indicate that there are good agreements between the experimental and numerical temperature distributions on those heat sinks. (C) 2015 Elsevier Ltd. All rights reserved.