The nanoporous structure of a membrane varies in a 3-dimensional (3-D) space and has remarkable influences on the filtration or desalination achieved, fouling potentials and therefore, the quality of yielded water. Knowledge of the 3-D nanoporous structure is thus vital to understanding and predicting its performance. A novel method by incorporating transmission electronic microtomography, image processing and 3-D reconstruction is introduced to characterize membranes with nano structures. The reconstruction algorithm allows for the visualization of 3-D nanoporous structure in a non-destructive way from any directions. This novel technique leads to in-depth understanding and accurate prediction of filtration performance. (C) 2009 Elsevier B.V. All rights reserved.