Two-dimensional, fully developed, convective heat transfer in compact passages is investigated numerically, incorporating the effects of the surface irregularities, to analyze the influence of these irregularities on fluid flow and heat transfer. This analysis helps to bring out the differences in the performance evaluation if regular cross sections are assumed in analyzing compact and mini channels. Forced convection in compact passages with an apparent rectangular shape is analyzed using a finite-difference method. The calculation is validated experimentally using Michelson interferometry. The numerical results for the channel, incorporating surface irregularities, are compared with those assuming a regular cross-sectional geometry. The results indicate that the coefficient of friction and the Nusselt number calculated for channels, considering the irregular cross section, are less than those predicted using an assumption of regular geometry. The results provide some insight into the reasons for the observed deviations in the comparisons. The observations are attributed to the influence of the surface irregularities on the relative dominance of the surface area to the cross-sectional area, which gets pronounced in compact passages. The findings suggest that some of the observed deviations in the performance of compact passages, compared to theoretical results, may be due to the use of regular geometries to define domain shapes while performing theoretical analysis.