In order to characterize the low surface brightness component in blue compact dwarf galaxies, we determine their structural parameters for eight objects by fitting a Sérsic law to the starburst-free regions of their deep B, V and R images using a two-dimensional fitting technique. We exclude the starburst emission by using color maps and Hα images. We use real data and ideal simulations to discuss the limitations of the technique and the uncertainties involved in fitting a Sérsic model, in particular, the limited portion of galaxy used in the fit and the sky-subtraction errors. We show that, by carefully masking out the starburst and performing a set of consistency checks, this 2D pixel-weighted fitting procedure is able to derive stable Sérsic parameters with small uncertainties, that could provide an important improvement in this kind of analysis. All galaxies in this sample show a red underlying component with low Sérsic indexes (n close to 1) and effective radii in agreement in the three bands, suggesting that they share similar structural properties.