The thermal protection system is a key element in atmospheric re-entry missions of aerospace vehicles. Usually, in the thermal load calculations, the analysis assumes that the vehicle has a smooth surface. However, discontinuities or imperfections are often present on the aerospace vehicle surfaces due to fabrication tolerances, sensor installations, spaces between the thermal protection plates, and differential expansion or ablation rates between non-similar materials. In the present work, rarefied hypersonic flows over two-and three-dimensional cavities at an altitude of 80 km in the Earth's atmosphere are studied numerically. To model flows in the transitional regime, where the validity of the Navier-Stokes equations is questionable, the direct simulation Monte Carlo method has been used. The primary goal is to assess the sensitivity of heat transfer, pressure, and skin-friction coefficients for a family of two-and threedimensional cavities defined by different length-to-depth ratios. The analysis shows that an assumption of twodimensionality plays a key role in the overprediction of the aerodynamic properties. Previous work using a continuum approach shows that two recirculation regions and flow attachment occurs when the length-to-depth ratio is equal to 14; however, the same phenomena are observed in the transitional regime when the cavity length-to-depth ratio is equal to 4. A study of the influence of the cavity width has also been conducted. It is shown that increasing the cavity width results in an augmentation of the surface aerothermodynamic quantities.