As one simple metamaterial, nanopatterns are often fabricated across a thin film so that the thermal transport can be manipulated. The etched sidewalls for these nanostructures are usually rough due to surface defects introduced during the nanofabrication, whereas the top and bottom film surfaces are smoother. In existing analytical models, the contrast between these surfaces has not been addressed and all boundaries are assumed to be diffusive for phonon reflection. In this paper, a new two-step approach to address this issue is proposed for phonon transport modeling of general thin-film-based structures. In this approach, the effective in-plane phonon mean free paths ( Λ ) are first modified from the bulk phonon MFPs to account for the influence of the top/bottom film surfaces, with possibly enhanced probability of specular phonon reflection at cryogenic temperatures. This Λ is further modified to include the scattering by etched sidewalls with almost completely diffusive phonon scattering. Such a two-step phonon mean free path modification yields almost identical results as frequency-dependent phonon Monte Carlo simulations for etched nanowires and representative nanoporous thin films. This simple yet accurate analytical model can be applied to general thin-film-based nanostructures to combine the phonon size effects along orthogonal directions. Key words: Two-step phonon mean free path modification; nanoporous thin film; rectangular nanowire. Nomenclature Abbreviations 2D Two-dimensional 3D Three-dimensional BTE Boltzmann transport equation MBL Mean beam length MC Monte Carlo MFP Mean free path RIE Reactive Ion Etching SOI Silicon on insulator Greek Symbols Average film-surface roughness (m) Included angle between the phonon traveling direction and the cross-plane direction (rad) Λ Bulk phonon mean free path (m) Λ Effective phonon mean free path (m) Λ Effective in-plane phonon mean free path along a solid thin film (m) Λ * Dimensionless ratio / Phonon wavelength (m) Porosity