Secondary electron emission (SEE) from inner linings of plasma chambers in electric thrusters for space propulsion can have a disruptive effect on device performance and efficiency. SEE is typically calculated using elastic and inelastic electron scattering theory by way of Monte Carlo simulations of independent electron trajectories. However, in practice the method can only be applied for ideally smooth surfaces and thin films, not representative of real material surfaces. Recently, micro-architected surfaces with micron-sized features have been proposed to mitigate SEE and ion-induced erosion in plasma-exposed thruster linings. In this paper, we propose an approach for calculating secondary electron yields from surfaces with arbitrarily-complex geometries using an extension of the ray tracing Monte Carlo (RTMC) technique. We study microfoam structures with varying porosities as representative micro-architected surfaces, and use RTMC to generate primary electron trajectories and track secondary electrons until their escape from the outer surface. Actual surfaces are represented as a discrete finite element meshes obtained from X-ray tomography images of tungsten microfoams. At the local level, primary rays impinging into surface elements produce daughter rays of secondary electrons whose number, energies and angular characteristics are set by pre-calculated tables of SEE yields and energies from ideally-flat surfaces. We find that these micro-architected geometries can reduce SEE by up to 50% with respect to flat surfaces depending on porosity and primary electron energy.