Optical coherence tomography (OCT) enables in vivo imaging of port wine stains (PWS) lesions. The knowledge of vascular structure and epidermal thickness (ET) of PWS may aid the objective diagnosis and optimal treatment. To obtain the structural parameters more rapidly and avoid user intervention, an automated algorithm of energy map is introduced based on intensity and edge information to extract the skin surface using dynamic programming method. Subsequently, an averaged A-scan analysis is performed to obtain the mean ET and the relative intensity of dermis indicating the corresponding vascular density. This approach is currently successfully applied in clinical diagnosis and shows promising guidance and assessment of PDT treatment.