In this study we investigate the stability of three-dimensional disturbances imposed on a heated or cooled two-dimensional boundary layer flow with a compliant surface. Such compliant surfaces may delay laminar to turbulent transition and reduce drag and noise levels in fluid flow. We exploit the multi-deck structure of the flow in the limit of large Reynolds numbers to analyse asymptotically the perturbed flow and to derive linear neutral results. A limited parametric study is carried out; the work extends that of Motsa et al. (2002) to three-dimensional disturbances.