Cloud and precipitation systems are simulated with a multi‐scale modeling framework (MMF) and compared over the Tropics and Subtropics against the Tropical Rainfall Measuring Mission (TRMM) Radar‐defined Precipitation Features (RPFs) product. A methodology, in close analogy to the TRMM RPFs, is developed to produce simulated precipitation features (PFs) from the output of the embedded two‐dimensional (2D) cloud‐resolving models (CRMs) within an MMF. Despite the limitations of 2D CRMs, the simulated population distribution, horizontal and vertical structure of PFs, and the geographical location and local rainfall contribution of mesoscale convective systems (MCSs) are in good agreement with the TRMM observations. However, some model discrepancies are found and can be identified and quantified within the PF distributions. Using model biases in relative population and rainfall contributions, PFs can be characterized into four size categories: small, medium to large, very large, and extremely large. Four different major mechanisms might account for the model biases in each different category: (1) the two‐dimensionality of the CRMs, (2) a positive convection‐wind‐evaporation feedback loop, (3) an artificial dynamic constraint in a bounded CRM domain with cyclic boundaries, and (4) the limited CRM domain size. The second and fourth mechanisms tend to contribute to the excessive tropical precipitation biases commonly found in most MMFs, whereas the other mechanisms reduce rainfall contributions from small and very large PFs. MMF sensitivity experiments with various CRM domain sizes and grid spacings showed that larger domains (higher resolutions) tend to shift PF populations toward larger (smaller) sizes.