In this paper we present a numerical approach to solve the Navier-Stokes equations for arbitrary vessel geometries by combining a Fourier-Spectral method with a direct forcing Immersed Boundary method which allows to consider solid-fluid interactions. The approach is applied to a paradigmatic setup motivated by the precession dynamo experiment currently under construction at Helmholtz-Zentrum Dresden-Rossendorf (HZDR). The experiment consists of a fluid filled cylinder rotating about 2 axes which induces a precession driven flow inside the cavity. The cylinder is also equipped with baffles at the end caps with adjustable penetration depth to impact the flow. The numerical details as well as simulation results for the spin-up and precession driven flow in a circular cylinder with additional baffles are presented. The results provide a first confirmation that the use of such baffles in the precession dynamo experiment is a useful way of influencing the flow, allowing more efficient driving without changing the known flow structure too much.