In a bid to accurately model structural behaviour of timber buildings in fire, a number of obstacles have been identified which must be fully understood before advanced computer modelling can accurately be used to represent physical behaviour. This paper discusses the obstacles, with suggestions on how to mitigate them, incorporating the challenges of using general purpose finite element software. The paper examines modelling with ANSYS, SAFIR and ABAQUS and the individual and collective challenges related to thermal analyses of timber structures in fire conditions. It considers the effects various model parameters (thermal and structural) may have on physical interpretation of experimental data in comparison with the accuracy of numerical solutions. In detail, the study looks at the effects of 1D and 2D heat transfer analyses, finite element mesh sizes, time steps and different thermal property approaches on thermal models of timber members in fires. It further recommends how best to model these structures using the different finite element software packages.