Molecular dynamics simulations of bubble nucleation in a heterogeneous system consisting of Lennard-Jones fluid and Lennard-Jones solid were performed. Periodic boundary conditions in two directions and wall potentials or fixed atoms forming the boundaries in the other direction were used. The effect of geometric defects on the nucleation rate and location of void formation was studied for indentations and protrusions with varying solid-fluid interactions using two ensembles. The first was constant temperature, number of atoms, and normal stress controlled by a wall potential above the fluid (NP_zzT). The second was constant flux of energy into the bottom layer of solid atoms, number of atoms, and normal stress (NP_zzq). For a given solid-fluid interaction in the constant temperature ensemble, defects on the order of 30 nm² had little effect on the calculated nucleation rates when compared with atomically smooth surfaces.