The need for more accessible energy resources makes shale formations increasingly important. Characterization of such low-permeability formations is complicated, due to the presence of multiscale features, and defies conventional methods. High-quality 3D imaging may be an ultimate solution for revealing the complexities of such porous media, but acquiring them is costly and time consuming. High-quality 2D images, on the other hand, are widely available. A novel three-step, multiscale, multiresolution reconstruction method is presented that directly uses 2D images in order to develop 3D models of shales. It uses a high-resolution 2D image representing the small-scale features to reproduce the nanopores and their network, a large scale, low-resolution 2D image to create the larger-scale characteristics, and generates stochastic realizations of the porous formation. The method is used to develop a model for a shale system for which the full 3D image is available and its properties can be computed. The predictions of the reconstructed models are in excellent agreement with the data. The method is, however, quite general and can be used for reconstructing models of other important heterogeneous materials and media. Two biological examples and from materials science are also reconstructed to demonstrate the generality of the method.