We present BTE-Barna (Boltzmann Transport Equation -Beyond the Rta for NAnosystems), a software package that extends the Monte Carlo (MC) module of the almaBTE solver of the Peierls-Boltzmann transport equation for phonons (PBTE) to work with nanosystems based on 2D materials with complex geometries. To properly capture how the phonon occupations evolve in momentum space as a result of scattering, we have supplemented the relaxation-time approximation with an implementation of the propagator for the full linearized version of the PBTE. The code can now find solutions for finite and extended devices under the effect of a thermal gradient, with isothermal reservoirs or with an arbitrary initial temperature distribution in space and time, writing out the temperature and heat flux distributions as well as their spectral decompositions. Besides the full deviational MC solver, a number of useful approximations for highly symmetric devices are also included.