The energy loss caused by biofouling is costing the marine operations millions of dollars because of lack of complete understanding of their roughness characteristics. Marine biofouling roughness is generally randomly distributed in space, and also varies in shape and texture. The common practice in hydrodynamic analysis is to ignore the details and express them simply by means of a representative length scale dimension. However, many recent studies have shown that this is not a satisfactory approach, particularly when the roughness height is large. The present research aims to develop a better measure of biofouling roughness by using an innovative image analysis technique to model and predict the related hydrodynamic phenomena. The proposed technique employs a combination of stochastic and triangulation techniques that are commonly used in image analysis. An overview of these techniques for surface topography measurement is provided. The present method uses two images of the surface, one from back lighting to spatially locate the roughness peaks and the second from side lighting to determine the height Information at each corresponding spatial location. Thus, a three-dimensional surface roughness distribution can be obtained. Results of some experiments on layers of taped surface and barnacle-laden surface suggests that this method can be used to measure flexible roughness height to within 10% accuracy, with possible improvement with a better lighting and camera resolution.