Optical coherence tomography (OCT) is commonly used to investigate the layers of the retina including retinal nerve fiber layer (RNFL) and retinal pigment epithelium (RPE). OCT images are altered by vessels on the retinal surface producing artefacts. We propose a new approach to compensate for these artefacts and enhance quality of OCT images. A total of 28 (20 normal and 8 glaucoma subjects) OCT images were obtained using Spectralis (Heidelberg, Germany). Shadows were detected along the image and compensated by the A-Scan intensity difference from surrounding non-affected areas. Images were then segmented and the area and thickness of RNFL and RPE were measured and compared. 10 subjects were tested twice to determine the effect of this on reproducibility of measurements. Shadow-suppressed images reflected the profile of the retinal layers more closely when assessed qualitatively, minimising distortion. The segmentation of RNFL and RPE thickness demonstrated a mean change of 2.4% ± 1 and 6% ± 1 from the original images. Much larger changes were observed in areas with vessels. Reproducibility of RNFL thickness was improved, specifically in the higher density vessel location, i.e. inferior and superior. Therefore, OCT images can be enhanced by an image processing procedure. Vessel artefacts may cause errors in assessment of RNFL thickness and are a source of variability, which has clinical implications for diseases such as glaucoma where subtle changes in RNFL need to be monitored accurately over time.