Advances in technologies associated with unmanned aerial vehicles (UAVs) have allowed researchers, farmers and agribusinesses to incorporate UAVs coupled with imaging systems into data collection and decision making. Multispectral imagery allows for a quantitative assessment of biophysical indicators or plant health status. What is needed now is a standardized workflow for the quantitative assessment of plant biophysical indicators using low-altitude, high-resolution, UAV-acquired multispectral imagery. With this need in mind, the authors developed and proposed a workflow for extracting plot-level vegetation index means from orthomosaics. As the use of UAVs and associated data collection activities expands, it will become increasingly important that data is being properly incorporated and utilized by ag professionals.