Context: The structural properties of the low surface brightness stellar host in blue compact dwarf galaxies are often studied by fitting r1/n models to the outer regions of their radial profiles. The limitations imposed by the presence of a large starburst emission overlapping the underlying component makes this kind of analysis a difficult task. Aims: We propose a two-dimensional fitting methodology in order to improve the extraction of the structural parameters of the LSB host. We discuss its advantages and weaknesses by using a set of simulated galaxies and compare the results for a sample of eight objects with those already obtained using a one-dimensional technique. Methods: We fit a PSF convolved Sérsic model to synthetic galaxies, and to real galaxy images in the B, V, R filters. We restrict the fit to the stellar host by masking out the starburst region and take special care to minimize the sky-subtraction uncertainties. In order to test the robustness and flexibility of the method, we carry out a set of fits with synthetic galaxies. Furthermore consistency checks are performed to assess the reliability and accuracy of the derived structural parameters. Results: The more accurate isolation of the starburst emission is the most important advantage and strength of the method. Thus, we fit the host galaxy in a range of surface brightness and in a portion of area larger than in previous published 1D fits with the same dataset. We obtain robust fits for all the sample galaxies, all of which, except one, show Sérsic indices n very close to 1, with good agreement in the three bands. These findings suggest that the stellar hosts in BCDs have near-exponential profiles, a result that will help us to understand the mechanisms that form and shape BCD galaxies, and how they relate to the other dwarf galaxy classes.