The quantification of physiological and biochemical parameters in coral branches require normalization to a stable factor such as the tissue biomass or surface area. 3D animation software (Gmax®) was evaluated for estimating the surface area of simple coral branches. The software was highly predictive of the known surface areas of small (20 – 60 mm long) plastic rods and cones (r2 > 0.99), and for small (30 – 60 mm) Acropora millepora branches (r2 = 0.98) whose surface area had been obtained using the traditional wax-weight method. Two normalization parameters, 3D modeled surface area and tissue biomass (measured as protein), were then compared for A. millepora branches collected in summer and winter. In winter, protein and surface area were correlated (r2 > 0.61) but not in summer, indicating that choice of normalizing parameter will influence the outcome of experimental analyses.