Beam collimation is an essential element for the successful running of a linear accelerator based free electron laser. The task of the collimation system is to protect the undulator modules against mis-steered beam and dark-current. This is achieved by a set of apertures limiting the succeeding transverse phase space volume and a magnetic dogleg structure for longitudinal phase space filtering. In the following the design of the BESSY FEL collimation section is described together with detailed simulation studies.