A fibrous filtering material is a kind of fiber assembly whose structure exhibits a three-dimensional (3D) network with dense microscopic open channels. The geometrical/morphological attributes, such as orientations, curvatures and compactness, of fibers in the network is the key to the filtration performance of the material. However, most of the previous studies were based on materials' 2D micro-images, which were unable to accurately measure these important 3D features of a filter's structure. In this paper, we present an imaging method to reconstruct the 3D structure of a fibrous filter from its optical microscopic images. Firstly, a series of images of the fiber assembly were captured at different depth layers as the stage moved vertically. Then a fusion image was established by extracting fiber edges from each layered image. Thirdly, the 3D coordinates of the fiber edges were determined using the sharpness/clarity of each edge pixel in the layered images. Finally, the 3D structure the fiber system was reconstructed through distance transformation based on the locations of fiber edges.