The mechanotransmission of fluid-induced forces in endothelial cells is a focal determinant of atherosclerosis. Understanding mechanotransmission is a key step towards developing endothelial-cell based therapies for cardiac diseases. Mechanotransmission is dependent on cell morphology, yet the effect of population morphological variation on mechanotransmission has not yet been examined. We have developed a set of morphological descriptors to quantify three-dimensional morphological variation in a population of human microvascular endothelial cells. From these data we determined quantitatively how the morphology of any cell compares to the overall population. Descriptors were used to generate virtual cells representative of the population morphologies. These virtual cells can be used as the spatial domain in a finite-element analysis. To the best of our knowledge, our study is the first to examine morphological variation in an EC population using a virtual cell approach.